g***@soe.ucsc.edu
2014-10-01 17:23:38 UTC
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Today's topic summary
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Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- GENCODE gtf [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cc7fa5fe83720933
- Transcription factors data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
- problems to access bigwikg on our server [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
- Need help with running BLAT on CentOS [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
- plotting read counts on the plus and minus strand [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
- A bug in table browser? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
- Genome Browser question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
- urgent!!! UCSC table browser has problem [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19eaa04b3efea16d
- Custom Track URL [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c2f1dacd7ed0ce5c
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Topic: GENCODE gtf
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cc7fa5fe83720933
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---------- 1 of 2 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 01 08:58AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/87a7ad63dc3e83b0
Hello Feliks,
Thank you for your questions about GENCODE Genes VM3 for mm10. The
newest update to the GENCODE Genes tracks is currently in our quality
assurance queue pending review by one our staff. A pre-release version
of this track is available on our test server,
http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM3.
You can intersect this GENCODE Genes track with the UCSC Genes track
available on our preview server following the same steps discussed by my
colleague Steve in previous emails, except replacing any mention of VM2
with VM3. However, please keep in mind that this our test server, and
that the data has not undergone our standard quality review process and
may be subject to change. We do hope to release this track to our public
website at http://genome.ucsc.edu/ soon, but I do not have a projected
date of when that might happen.
I hope this is helpful. If you have any further questions, please reply
to ***@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
On 9/17/14, 10:17 PM, Trakhtenberg, Feliks wrote:
---------- 2 of 2 ----------
From: "Trakhtenberg, Feliks" <***@childrens.harvard.edu>
Date: Oct 01 05:09PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/91189957a78d0c1a
thank you very much Matthew!
Ephraim
________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Wednesday, October 01, 2014 11:58 AM
To: Trakhtenberg, Feliks; ***@soe.ucsc.edu; 'Jonathan Casper'
Cc: ***@soe.ucsc.edu
Subject: Re: [genome] GENCODE gtf
Hello Feliks,
Thank you for your questions about GENCODE Genes VM3 for mm10. The newest update to the GENCODE Genes tracks is currently in our quality assurance queue pending review by one our staff. A pre-release version of this track is available on our test server, http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM3. You can intersect this GENCODE Genes track with the UCSC Genes track available on our preview server following the same steps discussed by my colleague Steve in previous emails, except replacing any mention of VM2 with VM3. However, please keep in mind that this our test server, and that the data has not undergone our standard quality review process and may be subject to change. We do hope to release this track to our public website at http://genome.ucsc.edu/ soon, but I do not have a projected date of when that might happen.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
Matthew Speir
UCSC Genome Bioinformatics Group
On 9/17/14, 10:17 PM, Trakhtenberg, Feliks wrote:
Hello,
Do you know the expected date when the Gencode M3 track would become available in the Table Browser?
I need it for using the intersection tool to identify UCSC Gene entries that do not overlap with the Gencode M3. I presume that uploading Gencode M3 GTF as a costume track to accomplish my goal would be problematic, because if it was as simple as that I guess it would already have been available in the Table Browser. Is this so? Or uploading it as a costume track may work for my purposes?
Thank you,
Ephraim
________________________________
From: Steve Heitner [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Thursday, September 11, 2014 1:06 PM
To: Trakhtenberg, Feliks; 'Jonathan Casper'
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello, Ephraim.
There is no specific order in a GTF file, so it should not be a problem to cat both files into a single file. Regarding the gene symbols being a part of the GTF output, this is a limitation of the way the Table Browser creates GTF output. If you would like the gene symbols to be a part of your GTF files, it will require some scripting on your part. We cannot provide advice on creating a script, but if you would like to use the Table Browser to provide output that will equate transcript ID to gene symbol and RefSeq ID for use in your script, you can follow these instructions:
For GENCODE:
1. As your output format, select âselected fields from primary and related tablesâ
2. Click the âget outputâ button
3. In the âSelect Fields from mm10.wgEncodeGencodeCompVM2â section, check the ânameâ and âname2â checkboxes
4. Click the âget outputâ button
For UCSC Genes:
1. As your output format, select âselected fields from primary and related tablesâ
2. Click the âget outputâ button
3. In the âSelect Fields from mm10.knownGeneâ section, check the ânameâ checkbox
4. In the âmm10.kgXref fieldsâ section, check the âgeneSymbolâ and ârefseqâ checkboxes
5. Click the âget outputâ button
Please contact us again at ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Trakhtenberg, Feliks [mailto:***@childrens.harvard.edu]
Sent: Sunday, September 07, 2014 1:11 PM
To: Jonathan Casper
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello,
Thank you for the advice. My goal is to predict novel genes/transcripts. I would like to compile a comprehensive mouse GTF, so that it does not turn out that the novel transcripts I find in my RNAseq have already been predicted in some major database. So, I thought that merging Gencode and UCSC Genes would provide such comprehensive set. Please let me know if this is insufficient.
Using the intersection tool you recommended below, even with no overlap selection, there are about 8k UCSC Gene transcripts not in the Gencode. Does the Table Browser have an option for merging these entries with the Gencode GTF? If not, would this command "cat out.gtf0[0-1] > merged.gtfâ produce a GTF that is compatible with the Table Browser?
The UCSC Gene GTF produced by the Table Browser reports gene and transcript IDs like this: gene_id "uc007aet.1"; transcript_id "uc007aet.1". However, it does not add to the entry the original database (e.g., RefSeq) accession nor gene name. Gencode GTF from the Table Browser also missing the gene names. How could I have the original database IDs and the gene names included in the UCSC Gene GTF produced by the Table Browser, and the gene names included in the Gencode GTF from the Table Browser?
Thanks,
Ephraim
________________________________
From: Jonathan Casper [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Thursday, August 14, 2014 9:10 PM
To: Trakhtenberg, Feliks
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: Re: [genome] GENCODE gtf
Hello Ephraim,
Our engineers comment that it is difficult to advise you on how to combine gene sets without knowing what you're trying to accomplish specifically. Different gene sets use different predictive models, making it hard to combine them in a scientifically meaningful way.
That said, you can use the UCSC Table Browser intersection tool to get a list of entries found in UCSC Genes but not in GENCODE.
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Use the following settings
clade: Mammal
genome: Mouse
assembly: Dec. 2011 (GRCm38/mm10)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: genome
3. Click the "intersection: create" button
4. On the "Intersect with UCSC Genes" page, set the following options:
group: Genes and Gene Predictions
track: GENCODE Genes VM2 (or V3, after it is released)
table: Basic (wgEncodeGencodeBasicVM2)
If you decide after reading the GENCODE track page that the Comprehensive table would be more useful to you, that is also an option.
5. Choose to return "All UCSC Genes records that have no overlap with GENCODE Genes VM2"
Note that the "no overlap" requirement here is fairly strict. You may wish to instead restrict to UCSC Genes records with no more than 50% overlap, for example, depending on your needs.
6. Click "submit" to return to the main Table Browser page
Note that the output format has been changed to BED. You can leave it in that way or change to GTF output. Just remember that the GTF output of the UCSC Table Browser will not exactly match the format of your GENCODE GTF file.
7. Click "get output"
We also have command line tools that will perform this kind of operation, but they are not designed to work with files in GTF. If you would like to explore this alternative, the relevant programs are called "featureBits" and "overlapSelect". They are available as part of the kent utilities on our download server at http://hgdownload.soe.ucsc.edu<http://hgdownload.soe.ucsc.edu/>. We provide precompiled binaries for these utilities at http://hgdownload.soe.ucsc.edu/admin/exe/, but only for a few computer architectures. You may need to download the source code and compile these tools yourself if your computer is not listed there. You can run each program by itself on a command line with no arguments to see a description of how to use it.
As for your other question, RefSeq is a curated set of transcripts drawn from GenBank. Like GenBank, it is quite possible that there will be RefSeq transcripts that are not represented in GENCODE.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> or genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Aug 12, 2014 at 11:26 AM, Trakhtenberg, Feliks <***@childrens.harvard.edu<mailto:***@childrens.harvard.edu>> wrote:
Hello,
Regarding your answer in point 4 below, is it possible to identify which UCSC Genes track transcripts from GenBank are not found in Ensembl and GENCODEv3? I would like to add them to the GENCODE gtf but do not want redundancies.
What about Refseq transcripts - might there also be some that are included in the UCSC Genes track but not in GENCODEv3, similar to how you explained about the GenBank transcripts?
Thank you,
Ephraim
________________________________
From: Steve Heitner [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Monday, August 11, 2014 5:46 PM
To: Trakhtenberg, Feliks; ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello, Ephraim.
To address all of your questions:
1. We recommend that you get the GTF files from GENCODE (http://www.gencodegenes.org). The Table Browser generates least common denominator GTFs for a lot of tracks and will not contain all of the information available in the official GENCODE GTFs.
2. The GENCODE mouse V3 track will hopefully be available this month (August 2014).
3. For information regarding the different GENCODE subtracks available at UCSC, I recommend reading through the description page at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM2.
4. Concerning whether or not the GENCODE track contains everything contained in the UCSC Genes track, I donât believe this can be answered definitively. The UCSC Genes track is based on GenBank while the GENCODE track is based on Ensembl. Because these are constructed using completely different methods, you will find in many cases that GenBank contains items that Ensembl does not and vice versa.
Please contact us again at ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Trakhtenberg, Feliks [mailto:***@childrens.harvard.edu<mailto:***@childrens.harvard.edu>]
Sent: Sunday, August 10, 2014 3:12 PM
To: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: [genome] GENCODE gtf
Hello,
I would appreciate if some could explain why the GENCODE gtf generated through the Table Browser is lacking gene, transcript, UTR, and Selenocysteine rows, which are present in the original GENCODE file. I plan to use this gtf for Tophat/Cufflinks RNA-seq analysis and just wanted to make sure I am using the right file.
When will the GENCODE mouse V3 be available through the Table Browser?
Is the table option called Comprehensive have the most of GENCODE transcripts, including those that are only predicted? Or other GENCODE tables, such as pseudogenes, have additional transcripts?
Is everything that is in the UCSC Gene table also included in the Comprehensive GENCODE table?
Thank you
Ephraim Trakhtenberg, PhD
--
--
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Topic: Transcription factors data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
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From: Brian Lee <***@soe.ucsc.edu>
Date: Oct 01 09:48AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fd4ab72f2863488a
Dear Andrea,
Thank you for using the UCSC Genome Browser and your question about ENCODE
data.
Please know the website for up-to-date information about the ENCODE project
is no longer hosted at www.genome.ucsc.edu/ENCODE, rather the current
ENCODE Consortium portal is located at https://www.encodeproject.org/ with
a mailing list address of encode-***@lists.stanford.edu. There are many
resources on the consortium portal page including information about
software tools for applying and analyzing ENCODE data:
https://www.encodeproject.org/software
However, on the UCSC Genome Browser you can still access ENCODE data from
the period of 2003 - 2012, and our ChIP-seq matrix helps to identify what
factors are available, and the summary page allows you to click to all
related results:
http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html
http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataSummaryHuman.html
Looking at the summary page you will see there are 3 experiments involving
MEF2A. By clicking through on the MEF2A link you can see there are 14 data
tracks available (by selecting the radio button for files on that page,
you can rather display all the files for immediate download). While these
are the raw data tracks of MEF2A data, if you are looking for a more
summarized display you can go to the uniform TFBS track that processed all
underlying files through a computational pipeline. You can read more (and
select only MEF2A from the "Filter by factor" option) on this page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3
Here is a session with the MEF2A uniform peaks displayed under the UCSC
Genes Track and the underlying raw data also displayed:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=MEF2A.Display
You can use our Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables, to
do an intersection on this displayed data. It involves several steps.
First you would create a custom track of the MEF2A regions and then
intersect that custom track with the Gene Prediction track of interest.
1. Go to the Table Browser and select hg19, group: Regulation, track: Txn
Factor ChIP, with region: genome selected
2. Click the filter: create button, and in "name does match" put the
following: MEF2A
3. Click the submit button and then change output format to custom track
and get output, and then click "get custom track in table browser"
You now have a custom track of all the MEF2A locations across the hg19
assembly. You can now do an intersection with a gene track.
1. Select group: Genes and Gene Predictions, track: UCSC Genes (or other
gene track)
2. Click the intersection: create button
3. Change the group on the intersection page to Custom Tracks and use the
track name just created in the last step, click submit
4. Change output to custom track and "get custom track in genome browser"
and you will now just have the UCSC genes that have MEF2A intersections
with their coding regions (it will exclude intersection with introns).
You can watch a tutorial about the Table Browser here to learn more about
creating custom tracks and doing further intersections:
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to ***@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genome-***@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genome Bioinformatics Group
On Sun, Sep 28, 2014 at 12:35 PM, Andrea Clocchiatti <
=============================================================================
Topic: problems to access bigwikg on our server
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
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---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 30 06:22PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ea8124079013fae4
Hello Eran,
I'm sorry to hear that you are having problems with your bigWig tracks.
There are several reasons why you might be having a problem; maybe your
system administrators have changed some network settings. We are happy to
help diagnose the problem for you, but it would help if we had the URL to
one of your bigWig files to test. You can email the URL to me privately to
avoid sharing it with the mailing list, if you like.
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genome-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:06 AM, Dr. Eyal Eran <
---------- 2 of 2 ----------
From: "Dr. Eyal Eran" <***@sheba.health.gov.il>
Date: Oct 01 07:59AM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e0164c2ce64651b5
Dear Jonathan and the UCSC team,
Thanks for the quick reply. I was able to temporary solve the problem by adding "www" before sheba-cancer.org.il. Both "sheba-cancer.org.il" and "www. sheba-cancer.org.il" domains should be registered for us and point to our server (and indeed in web browsers both are recognized), however the genome browser now shows the tracks only if I use the "www.sheba-cancer.org.il<http://www.sheba-cancer.org.il>" domain name for some reason. This should be a combined problem with a configuration change somewhere on the route, as the files were recognized before as I described in the first mail.
So for now at least we can workâŠ
Thanks again and let me know if you have any insight regarding this,
Eran
From: Jonathan Casper [mailto:***@soe.ucsc.edu]
Sent: Wednesday, October 01, 2014 4:22 AM
To: ×××× ×¢×š×, ×ך
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: Re: [genome] problems to access bigwikg on our server
Hello Eran,
I'm sorry to hear that you are having problems with your bigWig tracks. There are several reasons why you might be having a problem; maybe your system administrators have changed some network settings. We are happy to help diagnose the problem for you, but it would help if we had the URL to one of your bigWig files to test. You can email the URL to me privately to avoid sharing it with the mailing list, if you like.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> or genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:06 AM, Dr. Eyal Eran <***@sheba.health.gov.il<mailto:***@sheba.health.gov.il>> wrote:
Dear UCSC team,
In the last 10 days or so we can not see bigwig track in our UCSC sessions. Our local server
http://sheba-cancer.org.il (and all the track files in this server) are accessible, at least here in Israel from web browsers, but the UCSC browser does not display the tracks and complains about error in the Error column of the "Manage Custom Tracks" table. The error links states: "Could not open http://.........bw"
What can be the reason that the files are not accessible, although the local sever is up? Until 10 days ago every thing was fine.
Thnaks,
Eran
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--
=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 2 ----------
From: Aneesha Das <***@gmail.com>
Date: Oct 01 08:50AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/10f3f59e4bc99911
Hi Steve,
Thanks for replying. I am on vacation in Jakarta right now, so I will be
able to send you the files when I return to work on 7th October. Do let me
know if this is okay with you.
Regards,
Aneesha.
prefer that it doesnât go to the list.
questions. Questions sent to that address will be archived in a
publicly-accessible forum for the benefit of other users. If your question
http://pasa.sourceforge.net/).
-I../../../inc -I../../../../inc -c net.c
I have downloaded the compressed version of the program (blatSrc35.zip),
uncompressed the folder. But when I enter the blatSrc directory and type
not be found anywhere.
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 01 08:30AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/60c2b8f6d055e246
Hello, Aneesha.
Yes, this would be fine. Weâll look to hear from you when you return.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Aneesha Das [mailto:***@gmail.com]
Sent: Tuesday, September 30, 2014 8:21 PM
To: ***@soe.ucsc.edu
Cc: ***@soe.ucsc.edu
Subject: Re: Need help with running BLAT on CentOS
Hi Steve,
Thanks for replying. I am on vacation in Jakarta right now, so I will be able to send you the files when I return to work on 7th October. Do let me know if this is okay with you.
Regards,
Aneesha.
=============================================================================
Topic: plotting read counts on the plus and minus strand
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 30 06:16PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c55bb3a2507c85c9
Hello Assa,
Thank you for your question about plotting your - strand read counts below
the x axis of a graph. There is a way for you to do this, if you have your
read counts for the + and - strands in different bigWig (or bedGraph or
wiggle) files. When you load the custom track containing your read counts
on the - strand, there is a "negateValues" option that you can specify in
the track line (see
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html#wig_-_Signal_Graphing_Track_Settings).
This setting will automatically negate the read counts so that the positive
values are treated as negative and are displayed below the x axis.
You can also do this without the "negateValues" track setting by editing
your data so that the read counts for items on the - strand are negative
numbers instead of positive.
More information about the wiggle, bedGraph, and bigWig file formats is
available on our file formats page at
http://genome.ucsc.edu/FAQ/FAQformat.html. bigWig files are usually created
from wiggle or bedGraph files to store the data in a more compact format.
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genome-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:58 AM, Yeroslaviz, Assa <***@biochem.mpg.de
=============================================================================
Topic: A bug in table browser?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
=============================================================================
---------- 1 of 1 ----------
From: Robert Kuhn <***@soe.ucsc.edu>
Date: Sep 30 02:17PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/844e0a604c897aab
Hello, Peter,
I would add that you could get what you want by doing two queries in
the Table Browser. Set a filter on the "strand" field and query the
plus-strand for txStart and separately, query the minus-strand genes for
txEnd.
regards,
--b0b kuhn
ucsc genome bioinformatics group
=============================================================================
Topic: Genome Browser question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 30 12:41PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cf8433bd3a2d6fdc
Hello, Morgan.
Have you tried our In-Silico PCR tool? There is a web-based version
available at http://genome.ucsc.edu/cgi-bin/hgPcr. There is also a command
line version that is part of our BLAT suite and is free for non-commercial
use. It can be obtained from
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. Questions sent to that address will be archived in a
publicly-accessible forum for the benefit of other users. If your question
contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Preziosi, Morgan E [mailto:***@pitt.edu]
Sent: Monday, September 29, 2014 1:11 PM
To: ***@soe.ucsc.edu
Subject: [genome] Genome Browser question
Can Genome Browser be used to create In Situ probes? If so, how?
Thanks,
Morgan
--
=============================================================================
Topic: urgent!!! UCSC table browser has problem
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19eaa04b3efea16d
=============================================================================
---------- 1 of 1 ----------
From: Sophia <***@gmail.com>
Date: Sep 30 02:36PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/de9d63e58bbd63a
Hi,
I just notice that there is problem when I use table browser to get
the sequences.
I uploaded the BED file in 6-column format:
chrUextra 38 89 1ww7811245_1;27 0 +
.....
....
I want to get the sequences for each row (each row tells the genomic
position), but I found table browser can not get sequences for all of
the rows.
for example, in my BED file, there are 27 rows (representing 27
genomic locations), but the sequence file I got from table browser
only reported sequences for 9 rows.
Could you solve the problem?
the 27 rows are :
chrUextra 37 89 ww7811245_1;27 0 +
chrUextra 1189370 1189422 ww7811245_1;27 0 +
chrUextra 2170327 2170379 ww7811245_1;27 0 -
chrUextra 2444578 2444630 ww7811245_1;27 0 -
chrUextra 4027427 4027479 ww7811245_1;27 0 +
chrUextra 5963788 5963840 ww7811245_1;27 0 -
chrUextra 5978227 5978279 ww7811245_1;27 0 +
chrUextra 6324318 6324370 ww7811245_1;27 0 +
chrUextra 6820133 6820185 ww7811245_1;27 0 -
chrUextra 9612498 9612550 ww7811245_1;27 0 +
chrUextra 13843827 13843879 ww7811245_1;27 0 -
chrUextra 14670642 14670694 ww7811245_1;27 0 -
chrUextra 15067042 15067094 ww7811245_1;27 0 -
chrUextra 16885743 16885795 ww7811245_1;27 0 +
chrUextra 17444038 17444090 ww7811245_1;27 0 +
chrUextra 17960286 17960338 ww7811245_1;27 0 +
chrUextra 18391817 18391869 ww7811245_1;27 0 -
chrUextra 18488548 18488600 ww7811245_1;27 0 +
chrUextra 18580568 18580620 ww7811245_1;27 0 +
chrUextra 20801600 20801652 ww7811245_1;27 0 +
chrUextra 21201887 21201939 ww7811245_1;27 0 +
chrUextra 22632168 22632220 ww7811245_1;27 0 +
chrUextra 23495135 23495187 ww7811245_1;27 0 +
chrUextra 23739576 23739628 ww7811245_1;27 0 +
chrUextra 26119553 26119605 ww7811245_1;27 0 +
chrUextra 26535918 26535970 ww7811245_1;27 0 +
chrUextra 26611360 26611412 ww7811245_1;27 0 -
=============================================================================
Topic: Custom Track URL
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c2f1dacd7ed0ce5c
=============================================================================
---------- 1 of 1 ----------
From: Helen Li <***@ucsc.edu>
Date: Sep 30 11:19AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2c6dd1b07260a0e7
Hi,
I'm trying to upload a custom track and I've been doing so by uploading my
BED files. But how do I get a URL for my custom tracks so I can
share/upload into my trackhub?
Thanks,
Helen
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Today's topic summary
=============================================================================
Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- GENCODE gtf [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cc7fa5fe83720933
- Transcription factors data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
- problems to access bigwikg on our server [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
- Need help with running BLAT on CentOS [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
- plotting read counts on the plus and minus strand [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
- A bug in table browser? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
- Genome Browser question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
- urgent!!! UCSC table browser has problem [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19eaa04b3efea16d
- Custom Track URL [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c2f1dacd7ed0ce5c
=============================================================================
Topic: GENCODE gtf
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cc7fa5fe83720933
=============================================================================
---------- 1 of 2 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 01 08:58AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/87a7ad63dc3e83b0
Hello Feliks,
Thank you for your questions about GENCODE Genes VM3 for mm10. The
newest update to the GENCODE Genes tracks is currently in our quality
assurance queue pending review by one our staff. A pre-release version
of this track is available on our test server,
http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM3.
You can intersect this GENCODE Genes track with the UCSC Genes track
available on our preview server following the same steps discussed by my
colleague Steve in previous emails, except replacing any mention of VM2
with VM3. However, please keep in mind that this our test server, and
that the data has not undergone our standard quality review process and
may be subject to change. We do hope to release this track to our public
website at http://genome.ucsc.edu/ soon, but I do not have a projected
date of when that might happen.
I hope this is helpful. If you have any further questions, please reply
to ***@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
On 9/17/14, 10:17 PM, Trakhtenberg, Feliks wrote:
---------- 2 of 2 ----------
From: "Trakhtenberg, Feliks" <***@childrens.harvard.edu>
Date: Oct 01 05:09PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/91189957a78d0c1a
thank you very much Matthew!
Ephraim
________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Wednesday, October 01, 2014 11:58 AM
To: Trakhtenberg, Feliks; ***@soe.ucsc.edu; 'Jonathan Casper'
Cc: ***@soe.ucsc.edu
Subject: Re: [genome] GENCODE gtf
Hello Feliks,
Thank you for your questions about GENCODE Genes VM3 for mm10. The newest update to the GENCODE Genes tracks is currently in our quality assurance queue pending review by one our staff. A pre-release version of this track is available on our test server, http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM3. You can intersect this GENCODE Genes track with the UCSC Genes track available on our preview server following the same steps discussed by my colleague Steve in previous emails, except replacing any mention of VM2 with VM3. However, please keep in mind that this our test server, and that the data has not undergone our standard quality review process and may be subject to change. We do hope to release this track to our public website at http://genome.ucsc.edu/ soon, but I do not have a projected date of when that might happen.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
Matthew Speir
UCSC Genome Bioinformatics Group
On 9/17/14, 10:17 PM, Trakhtenberg, Feliks wrote:
Hello,
Do you know the expected date when the Gencode M3 track would become available in the Table Browser?
I need it for using the intersection tool to identify UCSC Gene entries that do not overlap with the Gencode M3. I presume that uploading Gencode M3 GTF as a costume track to accomplish my goal would be problematic, because if it was as simple as that I guess it would already have been available in the Table Browser. Is this so? Or uploading it as a costume track may work for my purposes?
Thank you,
Ephraim
________________________________
From: Steve Heitner [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Thursday, September 11, 2014 1:06 PM
To: Trakhtenberg, Feliks; 'Jonathan Casper'
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello, Ephraim.
There is no specific order in a GTF file, so it should not be a problem to cat both files into a single file. Regarding the gene symbols being a part of the GTF output, this is a limitation of the way the Table Browser creates GTF output. If you would like the gene symbols to be a part of your GTF files, it will require some scripting on your part. We cannot provide advice on creating a script, but if you would like to use the Table Browser to provide output that will equate transcript ID to gene symbol and RefSeq ID for use in your script, you can follow these instructions:
For GENCODE:
1. As your output format, select âselected fields from primary and related tablesâ
2. Click the âget outputâ button
3. In the âSelect Fields from mm10.wgEncodeGencodeCompVM2â section, check the ânameâ and âname2â checkboxes
4. Click the âget outputâ button
For UCSC Genes:
1. As your output format, select âselected fields from primary and related tablesâ
2. Click the âget outputâ button
3. In the âSelect Fields from mm10.knownGeneâ section, check the ânameâ checkbox
4. In the âmm10.kgXref fieldsâ section, check the âgeneSymbolâ and ârefseqâ checkboxes
5. Click the âget outputâ button
Please contact us again at ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Trakhtenberg, Feliks [mailto:***@childrens.harvard.edu]
Sent: Sunday, September 07, 2014 1:11 PM
To: Jonathan Casper
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello,
Thank you for the advice. My goal is to predict novel genes/transcripts. I would like to compile a comprehensive mouse GTF, so that it does not turn out that the novel transcripts I find in my RNAseq have already been predicted in some major database. So, I thought that merging Gencode and UCSC Genes would provide such comprehensive set. Please let me know if this is insufficient.
Using the intersection tool you recommended below, even with no overlap selection, there are about 8k UCSC Gene transcripts not in the Gencode. Does the Table Browser have an option for merging these entries with the Gencode GTF? If not, would this command "cat out.gtf0[0-1] > merged.gtfâ produce a GTF that is compatible with the Table Browser?
The UCSC Gene GTF produced by the Table Browser reports gene and transcript IDs like this: gene_id "uc007aet.1"; transcript_id "uc007aet.1". However, it does not add to the entry the original database (e.g., RefSeq) accession nor gene name. Gencode GTF from the Table Browser also missing the gene names. How could I have the original database IDs and the gene names included in the UCSC Gene GTF produced by the Table Browser, and the gene names included in the Gencode GTF from the Table Browser?
Thanks,
Ephraim
________________________________
From: Jonathan Casper [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Thursday, August 14, 2014 9:10 PM
To: Trakhtenberg, Feliks
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: Re: [genome] GENCODE gtf
Hello Ephraim,
Our engineers comment that it is difficult to advise you on how to combine gene sets without knowing what you're trying to accomplish specifically. Different gene sets use different predictive models, making it hard to combine them in a scientifically meaningful way.
That said, you can use the UCSC Table Browser intersection tool to get a list of entries found in UCSC Genes but not in GENCODE.
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Use the following settings
clade: Mammal
genome: Mouse
assembly: Dec. 2011 (GRCm38/mm10)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: genome
3. Click the "intersection: create" button
4. On the "Intersect with UCSC Genes" page, set the following options:
group: Genes and Gene Predictions
track: GENCODE Genes VM2 (or V3, after it is released)
table: Basic (wgEncodeGencodeBasicVM2)
If you decide after reading the GENCODE track page that the Comprehensive table would be more useful to you, that is also an option.
5. Choose to return "All UCSC Genes records that have no overlap with GENCODE Genes VM2"
Note that the "no overlap" requirement here is fairly strict. You may wish to instead restrict to UCSC Genes records with no more than 50% overlap, for example, depending on your needs.
6. Click "submit" to return to the main Table Browser page
Note that the output format has been changed to BED. You can leave it in that way or change to GTF output. Just remember that the GTF output of the UCSC Table Browser will not exactly match the format of your GENCODE GTF file.
7. Click "get output"
We also have command line tools that will perform this kind of operation, but they are not designed to work with files in GTF. If you would like to explore this alternative, the relevant programs are called "featureBits" and "overlapSelect". They are available as part of the kent utilities on our download server at http://hgdownload.soe.ucsc.edu<http://hgdownload.soe.ucsc.edu/>. We provide precompiled binaries for these utilities at http://hgdownload.soe.ucsc.edu/admin/exe/, but only for a few computer architectures. You may need to download the source code and compile these tools yourself if your computer is not listed there. You can run each program by itself on a command line with no arguments to see a description of how to use it.
As for your other question, RefSeq is a curated set of transcripts drawn from GenBank. Like GenBank, it is quite possible that there will be RefSeq transcripts that are not represented in GENCODE.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> or genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Aug 12, 2014 at 11:26 AM, Trakhtenberg, Feliks <***@childrens.harvard.edu<mailto:***@childrens.harvard.edu>> wrote:
Hello,
Regarding your answer in point 4 below, is it possible to identify which UCSC Genes track transcripts from GenBank are not found in Ensembl and GENCODEv3? I would like to add them to the GENCODE gtf but do not want redundancies.
What about Refseq transcripts - might there also be some that are included in the UCSC Genes track but not in GENCODEv3, similar to how you explained about the GenBank transcripts?
Thank you,
Ephraim
________________________________
From: Steve Heitner [***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>]
Sent: Monday, August 11, 2014 5:46 PM
To: Trakhtenberg, Feliks; ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: RE: [genome] GENCODE gtf
Hello, Ephraim.
To address all of your questions:
1. We recommend that you get the GTF files from GENCODE (http://www.gencodegenes.org). The Table Browser generates least common denominator GTFs for a lot of tracks and will not contain all of the information available in the official GENCODE GTFs.
2. The GENCODE mouse V3 track will hopefully be available this month (August 2014).
3. For information regarding the different GENCODE subtracks available at UCSC, I recommend reading through the description page at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=wgEncodeGencodeVM2.
4. Concerning whether or not the GENCODE track contains everything contained in the UCSC Genes track, I donât believe this can be answered definitively. The UCSC Genes track is based on GenBank while the GENCODE track is based on Ensembl. Because these are constructed using completely different methods, you will find in many cases that GenBank contains items that Ensembl does not and vice versa.
Please contact us again at ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Trakhtenberg, Feliks [mailto:***@childrens.harvard.edu<mailto:***@childrens.harvard.edu>]
Sent: Sunday, August 10, 2014 3:12 PM
To: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: [genome] GENCODE gtf
Hello,
I would appreciate if some could explain why the GENCODE gtf generated through the Table Browser is lacking gene, transcript, UTR, and Selenocysteine rows, which are present in the original GENCODE file. I plan to use this gtf for Tophat/Cufflinks RNA-seq analysis and just wanted to make sure I am using the right file.
When will the GENCODE mouse V3 be available through the Table Browser?
Is the table option called Comprehensive have the most of GENCODE transcripts, including those that are only predicted? Or other GENCODE tables, such as pseudogenes, have additional transcripts?
Is everything that is in the UCSC Gene table also included in the Comprehensive GENCODE table?
Thank you
Ephraim Trakhtenberg, PhD
--
--
--
--
=============================================================================
Topic: Transcription factors data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
=============================================================================
---------- 1 of 1 ----------
From: Brian Lee <***@soe.ucsc.edu>
Date: Oct 01 09:48AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fd4ab72f2863488a
Dear Andrea,
Thank you for using the UCSC Genome Browser and your question about ENCODE
data.
Please know the website for up-to-date information about the ENCODE project
is no longer hosted at www.genome.ucsc.edu/ENCODE, rather the current
ENCODE Consortium portal is located at https://www.encodeproject.org/ with
a mailing list address of encode-***@lists.stanford.edu. There are many
resources on the consortium portal page including information about
software tools for applying and analyzing ENCODE data:
https://www.encodeproject.org/software
However, on the UCSC Genome Browser you can still access ENCODE data from
the period of 2003 - 2012, and our ChIP-seq matrix helps to identify what
factors are available, and the summary page allows you to click to all
related results:
http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html
http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataSummaryHuman.html
Looking at the summary page you will see there are 3 experiments involving
MEF2A. By clicking through on the MEF2A link you can see there are 14 data
tracks available (by selecting the radio button for files on that page,
you can rather display all the files for immediate download). While these
are the raw data tracks of MEF2A data, if you are looking for a more
summarized display you can go to the uniform TFBS track that processed all
underlying files through a computational pipeline. You can read more (and
select only MEF2A from the "Filter by factor" option) on this page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3
Here is a session with the MEF2A uniform peaks displayed under the UCSC
Genes Track and the underlying raw data also displayed:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=MEF2A.Display
You can use our Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables, to
do an intersection on this displayed data. It involves several steps.
First you would create a custom track of the MEF2A regions and then
intersect that custom track with the Gene Prediction track of interest.
1. Go to the Table Browser and select hg19, group: Regulation, track: Txn
Factor ChIP, with region: genome selected
2. Click the filter: create button, and in "name does match" put the
following: MEF2A
3. Click the submit button and then change output format to custom track
and get output, and then click "get custom track in table browser"
You now have a custom track of all the MEF2A locations across the hg19
assembly. You can now do an intersection with a gene track.
1. Select group: Genes and Gene Predictions, track: UCSC Genes (or other
gene track)
2. Click the intersection: create button
3. Change the group on the intersection page to Custom Tracks and use the
track name just created in the last step, click submit
4. Change output to custom track and "get custom track in genome browser"
and you will now just have the UCSC genes that have MEF2A intersections
with their coding regions (it will exclude intersection with introns).
You can watch a tutorial about the Table Browser here to learn more about
creating custom tracks and doing further intersections:
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to ***@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genome-***@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genome Bioinformatics Group
On Sun, Sep 28, 2014 at 12:35 PM, Andrea Clocchiatti <
=============================================================================
Topic: problems to access bigwikg on our server
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 30 06:22PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ea8124079013fae4
Hello Eran,
I'm sorry to hear that you are having problems with your bigWig tracks.
There are several reasons why you might be having a problem; maybe your
system administrators have changed some network settings. We are happy to
help diagnose the problem for you, but it would help if we had the URL to
one of your bigWig files to test. You can email the URL to me privately to
avoid sharing it with the mailing list, if you like.
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genome-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:06 AM, Dr. Eyal Eran <
---------- 2 of 2 ----------
From: "Dr. Eyal Eran" <***@sheba.health.gov.il>
Date: Oct 01 07:59AM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e0164c2ce64651b5
Dear Jonathan and the UCSC team,
Thanks for the quick reply. I was able to temporary solve the problem by adding "www" before sheba-cancer.org.il. Both "sheba-cancer.org.il" and "www. sheba-cancer.org.il" domains should be registered for us and point to our server (and indeed in web browsers both are recognized), however the genome browser now shows the tracks only if I use the "www.sheba-cancer.org.il<http://www.sheba-cancer.org.il>" domain name for some reason. This should be a combined problem with a configuration change somewhere on the route, as the files were recognized before as I described in the first mail.
So for now at least we can workâŠ
Thanks again and let me know if you have any insight regarding this,
Eran
From: Jonathan Casper [mailto:***@soe.ucsc.edu]
Sent: Wednesday, October 01, 2014 4:22 AM
To: ×××× ×¢×š×, ×ך
Cc: ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>
Subject: Re: [genome] problems to access bigwikg on our server
Hello Eran,
I'm sorry to hear that you are having problems with your bigWig tracks. There are several reasons why you might be having a problem; maybe your system administrators have changed some network settings. We are happy to help diagnose the problem for you, but it would help if we had the URL to one of your bigWig files to test. You can email the URL to me privately to avoid sharing it with the mailing list, if you like.
I hope this is helpful. If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@soe.ucsc.edu> or genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:06 AM, Dr. Eyal Eran <***@sheba.health.gov.il<mailto:***@sheba.health.gov.il>> wrote:
Dear UCSC team,
In the last 10 days or so we can not see bigwig track in our UCSC sessions. Our local server
http://sheba-cancer.org.il (and all the track files in this server) are accessible, at least here in Israel from web browsers, but the UCSC browser does not display the tracks and complains about error in the Error column of the "Manage Custom Tracks" table. The error links states: "Could not open http://.........bw"
What can be the reason that the files are not accessible, although the local sever is up? Until 10 days ago every thing was fine.
Thnaks,
Eran
[Loading Image...
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=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 2 ----------
From: Aneesha Das <***@gmail.com>
Date: Oct 01 08:50AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/10f3f59e4bc99911
Hi Steve,
Thanks for replying. I am on vacation in Jakarta right now, so I will be
able to send you the files when I return to work on 7th October. Do let me
know if this is okay with you.
Regards,
Aneesha.
gcc -v
uname -a
Then please send us the file output from the first command and the output
from the other two commands. You can send it directly to me if you woulduname -a
Then please send us the file output from the first command and the output
prefer that it doesnât go to the list.
questions. Questions sent to that address will be archived in a
publicly-accessible forum for the benefit of other users. If your question
Hi Dr.Kent,
I was trying to install the BLAT software on a machine with CentOS system
1.I uncompressed the blat folder in the PASA main directory.
2. Copied the entire PASA directory to the /usr/local/bin folder as per
the instructions available in the PASA installation page (I was trying to install the BLAT software on a machine with CentOS system
1.I uncompressed the blat folder in the PASA main directory.
2. Copied the entire PASA directory to the /usr/local/bin folder as per
http://pasa.sourceforge.net/).
3. Logged into the blatSrc folder.
4. Obtained the MACHTYPE of the machine by typing
($MACHTYPE, x86_64-redhat-linux-gnu) and exported it.4. Obtained the MACHTYPE of the machine by typing
5. Then I entered the lib directory within the blatSrc folder and typed
'make' for which the following error message was obtained.gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc-I../../../inc -I../../../../inc -c net.c
cc1: warnings being treated as errors
net.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ
differ in signednessnet.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ
/usr/include/sys/socket.h:190: note: expected âsocklen_t * __restrict__â
but argument is of type âint *ânet.c:115: error: pointer targets in passing argument 3 of âacceptâ
differ in signedness/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *ânet.c:130: error: pointer targets in passing argument 3 of âacceptâ
differ in signedness/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *âAneesha.
Looks like you need to setenv MACHTYPE, and also do a make in the lib
directory. Instructions for this should be in the README.Looks like you need to setenv MACHTYPE, and also do a make in the lib
Dear Dr.Kent,
I work in Dr.Saikat Chakrabarti's lab at the CSIR-Indian Institute of
Chemical Biology. I have been trying to install BLAT in CentOS 5.8 server.I work in Dr.Saikat Chakrabarti's lab at the CSIR-Indian Institute of
I have downloaded the compressed version of the program (blatSrc35.zip),
uncompressed the folder. But when I enter the blatSrc directory and type
make[1]: Entering directory
`/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make[1]: *** No rule to make target `../lib//jkweb.a', needed by `blat'.
Stop.`/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make[1]: *** No rule to make target `../lib//jkweb.a', needed by `blat'.
make[1]: Leaving directory
`/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'make: *** [all] Error 2
I had made a directory using the $MACHTYPE variable
(x86_64-redhat-linux-gnu) in the lib directory, but the file jkweb.a couldI had made a directory using the $MACHTYPE variable
not be found anywhere.
I badly need help with the installation and running of this program
(which is a part of the PASA pipeline, which I am trying to run).---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 01 08:30AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/60c2b8f6d055e246
Hello, Aneesha.
Yes, this would be fine. Weâll look to hear from you when you return.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Aneesha Das [mailto:***@gmail.com]
Sent: Tuesday, September 30, 2014 8:21 PM
To: ***@soe.ucsc.edu
Cc: ***@soe.ucsc.edu
Subject: Re: Need help with running BLAT on CentOS
Hi Steve,
Thanks for replying. I am on vacation in Jakarta right now, so I will be able to send you the files when I return to work on 7th October. Do let me know if this is okay with you.
Regards,
Aneesha.
=============================================================================
Topic: plotting read counts on the plus and minus strand
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 30 06:16PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c55bb3a2507c85c9
Hello Assa,
Thank you for your question about plotting your - strand read counts below
the x axis of a graph. There is a way for you to do this, if you have your
read counts for the + and - strands in different bigWig (or bedGraph or
wiggle) files. When you load the custom track containing your read counts
on the - strand, there is a "negateValues" option that you can specify in
the track line (see
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html#wig_-_Signal_Graphing_Track_Settings).
This setting will automatically negate the read counts so that the positive
values are treated as negative and are displayed below the x axis.
You can also do this without the "negateValues" track setting by editing
your data so that the read counts for items on the - strand are negative
numbers instead of positive.
More information about the wiggle, bedGraph, and bigWig file formats is
available on our file formats page at
http://genome.ucsc.edu/FAQ/FAQformat.html. bigWig files are usually created
from wiggle or bedGraph files to store the data in a more compact format.
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genome-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 30, 2014 at 8:58 AM, Yeroslaviz, Assa <***@biochem.mpg.de
=============================================================================
Topic: A bug in table browser?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
=============================================================================
---------- 1 of 1 ----------
From: Robert Kuhn <***@soe.ucsc.edu>
Date: Sep 30 02:17PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/844e0a604c897aab
Hello, Peter,
I would add that you could get what you want by doing two queries in
the Table Browser. Set a filter on the "strand" field and query the
plus-strand for txStart and separately, query the minus-strand genes for
txEnd.
regards,
--b0b kuhn
ucsc genome bioinformatics group
=============================================================================
Topic: Genome Browser question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 30 12:41PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cf8433bd3a2d6fdc
Hello, Morgan.
Have you tried our In-Silico PCR tool? There is a web-based version
available at http://genome.ucsc.edu/cgi-bin/hgPcr. There is also a command
line version that is part of our BLAT suite and is free for non-commercial
use. It can be obtained from
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. Questions sent to that address will be archived in a
publicly-accessible forum for the benefit of other users. If your question
contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Preziosi, Morgan E [mailto:***@pitt.edu]
Sent: Monday, September 29, 2014 1:11 PM
To: ***@soe.ucsc.edu
Subject: [genome] Genome Browser question
Can Genome Browser be used to create In Situ probes? If so, how?
Thanks,
Morgan
--
=============================================================================
Topic: urgent!!! UCSC table browser has problem
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19eaa04b3efea16d
=============================================================================
---------- 1 of 1 ----------
From: Sophia <***@gmail.com>
Date: Sep 30 02:36PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/de9d63e58bbd63a
Hi,
I just notice that there is problem when I use table browser to get
the sequences.
I uploaded the BED file in 6-column format:
chrUextra 38 89 1ww7811245_1;27 0 +
.....
....
I want to get the sequences for each row (each row tells the genomic
position), but I found table browser can not get sequences for all of
the rows.
for example, in my BED file, there are 27 rows (representing 27
genomic locations), but the sequence file I got from table browser
only reported sequences for 9 rows.
Could you solve the problem?
the 27 rows are :
chrUextra 37 89 ww7811245_1;27 0 +
chrUextra 1189370 1189422 ww7811245_1;27 0 +
chrUextra 2170327 2170379 ww7811245_1;27 0 -
chrUextra 2444578 2444630 ww7811245_1;27 0 -
chrUextra 4027427 4027479 ww7811245_1;27 0 +
chrUextra 5963788 5963840 ww7811245_1;27 0 -
chrUextra 5978227 5978279 ww7811245_1;27 0 +
chrUextra 6324318 6324370 ww7811245_1;27 0 +
chrUextra 6820133 6820185 ww7811245_1;27 0 -
chrUextra 9612498 9612550 ww7811245_1;27 0 +
chrUextra 13843827 13843879 ww7811245_1;27 0 -
chrUextra 14670642 14670694 ww7811245_1;27 0 -
chrUextra 15067042 15067094 ww7811245_1;27 0 -
chrUextra 16885743 16885795 ww7811245_1;27 0 +
chrUextra 17444038 17444090 ww7811245_1;27 0 +
chrUextra 17960286 17960338 ww7811245_1;27 0 +
chrUextra 18391817 18391869 ww7811245_1;27 0 -
chrUextra 18488548 18488600 ww7811245_1;27 0 +
chrUextra 18580568 18580620 ww7811245_1;27 0 +
chrUextra 20801600 20801652 ww7811245_1;27 0 +
chrUextra 21201887 21201939 ww7811245_1;27 0 +
chrUextra 22632168 22632220 ww7811245_1;27 0 +
chrUextra 23495135 23495187 ww7811245_1;27 0 +
chrUextra 23739576 23739628 ww7811245_1;27 0 +
chrUextra 26119553 26119605 ww7811245_1;27 0 +
chrUextra 26535918 26535970 ww7811245_1;27 0 +
chrUextra 26611360 26611412 ww7811245_1;27 0 -
=============================================================================
Topic: Custom Track URL
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c2f1dacd7ed0ce5c
=============================================================================
---------- 1 of 1 ----------
From: Helen Li <***@ucsc.edu>
Date: Sep 30 11:19AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2c6dd1b07260a0e7
Hi,
I'm trying to upload a custom track and I've been doing so by uploading my
BED files. But how do I get a URL for my custom tracks so I can
share/upload into my trackhub?
Thanks,
Helen
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