Digest for genome@soe.ucsc.edu - 7 updates in 4 topics

g***@soe.ucsc.edu

2014-09-17 17:16:27 UTC

chr1 1288539 1288540
and get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from

previous questions for submission of a list of positions I used the

#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
exonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file to

interrogate with the protein IDs. May I trouble you for insight as to
settings to reveal gene names associated with these positions?

--

---------- 2 of 2 ----------
From: "LaFramboise, William A" <***@upmc.edu>
Date: Sep 17 11:22AM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/538248bdc1d5a656

Thanks Steve.
Bill

-----Original Message-----
From: Steve Heitner [mailto:***@soe.ucsc.edu]
Sent: Tuesday, September 16, 2014 5:36 PM
To: LaFramboise, William A; ***@soe.ucsc.edu; 'Matthew Speir'
Subject: RE: [genome] should be simple in table browser

Hello, Bill.

With the exception of retrieving sequence from the Table Browser where you can add an optional description field into your input which gets inserted into the FASTA headers of your output, the Table Browser is not designed to include any input in the output. You will have to design a script to parse and insert the appropriate information into your output.

You may also consider checking out Galaxy (https://usegalaxy.org/) to see if they have any tools that would be useful to you in this regard.

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 toÂ genome-***@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

-----Original Message-----
From: LaFramboise, William A [mailto:***@upmc.edu]
Sent: Sunday, September 14, 2014 5:25 AM
To: ***@soe.ucsc.edu; Matthew Speir
Subject: RE: [genome] should be simple in table browser

This solution worked nicely. One niggling issue--- I get many outputs (multiple variants) for my entries but cannot align them with my original entries since none of my input is retained in the output file. Is there a simple way to retain one of my entry coordinates or add a series number to the input to sort and align the output?

Thanks,

Bill.
________________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Friday, September 12, 2014 6:41 PM
To: LaFramboise, William A; ***@soe.ucsc.edu
Subject: Re: [genome] should be simple in table browser

Hi Bill,

Thank you for your question about getting gene symbols as part of your from the Table Browser. You are on the right track with your current Table Browser settings, and the only issue is your output settings. The reason you are not getting gene symbols as part of your output is because these are not stored in the knownGene table for the UCSC Genes track, but instead stored in a linked table. When you select the output option "all fields from selected table", you are only getting the information contained in the knownGene table. I recommend using the "selected fields from primary and related tables" output option. After you click "get output", you will be taken to another page where you will be able to select fields from both the knownGene table and various linked tables that you want as part of your output. On this page, select those fields from the "Select Fields from hg19.knownGene" section that you are interested in. In the "hg19.kgXref fields" section, you will find a number of alternative IDs for the transcripts in the knownGene table. Check the box next to "geneSymbol", and any other IDs you are interested in. Finally, click "get output". Your output will consist of the fields you selected as columns in order starting from the top of the "hg19.knownGene" section. While this output option doesn't necessarily format your output in a terribly useful way, you can use a simple UNIX command line utility such as awk to rearrange the columns however you want.

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

chr1 1288539 1288540
and get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from
exonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file
to

interrogate with the protein IDs. May I trouble you for insight as to settings to reveal gene names associated with these positions?

--

=============================================================================
Topic: Question regarding the UCSC genome browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
=============================================================================

---------- 1 of 1 ----------
From: "Jain, Nitika" <***@iupui.edu>
Date: Sep 16 04:41PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cb5cd8264e079be8

Dear Sir/ Madam

I have been trying to find genes for the probe sets in a batch from
UCSC but not able to do so. I could only find the gene for one probeset
at a time. Kindly help me regarding that, as I have a list of more
than 1000 probesets and it is not possible to work on them one at a
time.

Thank you

Dr Nitika Jain

=============================================================================
Topic: Converting genomic coordinates to cDNA coordinates
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c14272278f44ff51
=============================================================================

---------- 1 of 2 ----------
From: Margaret Hoang <***@gmail.com>
Date: Sep 16 12:21PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f220746531f9ded7

Hi, I have the following information for mutations in GRCh37/hg19:

1. Transcript Accession
2. Gene Accession
3. Genomic Coordinate and Base sequence (i.e. g.chr1:2000-2000C>T)

Iâd like to express this as cDNA coordinates including the transcriptional base (i.e. c.190G>A).

Do you have suggestions on how to do this?

Thank you,
Margaret

~~~
Margaret Hoang, Ph.D.
Postdoctoral Fellow
Ludwig Center for Cancer Genetics and Therapeutics
The Sidney Kimmel Comprehensive Cancer Center
Johns Hopkins University, School of Medicine
1650 Orleans St., CRB1 Room 520, Baltimore, MD 21231
Office: 410-955-8878
Fax: 410-955-0548
Email: ***@gmail.com

---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 01:39PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/346e2aa3eec40944

Hello Margaret,

Thank you for your question about converting genomic variants into other
formats. One of our engineers suggests that the following tool may provide
almost exactly what you need: https://mutalyzer.nl/positionConverter. You
would need to make some minor changes: the "g." should appear after the
colon (e.g., g.chr1:2000-2000C>T --> chr1:g.2000-2000C>T).

You may also be interested in our Variant Annotation Integrator (VAI) at
http://genome.ucsc.edu/cgi-bin/hgVai. With a list of variants in pgSNP or
VCF format, the VAI can provide coordinates for the variants in cDNA and
CDS for a variety of gene/transcript sets along with consequent changes to
the transcriptional base(s).

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

=============================================================================
Topic: mysql connction
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/86e14d7cc5ce3b79
=============================================================================

---------- 1 of 2 ----------
From: "Schmidt, Mike A" <***@med.miami.edu>
Date: Sep 16 07:17PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e08d39ae49d2da31

Hi,
I was trying to connect to your DB using the mysql client on my Windows7-64 machine but had no luck. See below...
[cid:***@01CFD1C1.5CDFAE10]

Any idea what I am doing wrong? I followed your instructions on:
http://genome.ucsc.edu/goldenPath/help/mysql.html

Thanks much
Mike Schmidt

---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 12:31PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/69f6897e075891af

Hello Mike,

Thank you for your question about connecting to our public mysql server.
The problem appears to be that you are connecting to our mysql server as
"genome" without specifying a password, but mysql decides you're using a
password all the same (using password: YES). Do you have a mysql
configuration file set up with a default password? That might be
interfering. You can get around this by connecting as user "genomep" and
specifying the password "password".

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 16, 2014 at 12:17 PM, Schmidt, Mike A <***@med.miami.edu>
wrote:

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g***@soe.ucsc.edu

2014-09-20 17:07:11 UTC

Permalink

=============================================================================
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

- UCSC [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/35be3feb299b871b
- UCSC gene annotation update? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a9074b22278e81a1
- Release 6 Drosophila melanogaster genome? [3 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21d0fb05ff11cc47
- Question regarding the UCSC genome browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f

=============================================================================
Topic: UCSC
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/35be3feb299b871b
=============================================================================

---------- 1 of 2 ----------
From: <***@lumc.nl>
Date: Sep 19 05:44PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f0bf034d02da5ae5

Dear Sir or Madam,

I'm trying to fetch genomic data from UCSC via R (Biomart), and I've been having problems getting it for a few hours now. Could it be there is some maintenance going on?

Thank you very much!

Best Regards,
Matthias

---------- 2 of 2 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 19 04:01PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cd7f58d19b282581

Hi Matthias,

Thank you for your question about the UCSC Genome Browser. We are not
doing any maintenance on our public MySQL server, nor am I aware of any
issues with this server. Are you still experiencing issues at this time?

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

=============================================================================
Topic: UCSC gene annotation update?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a9074b22278e81a1
=============================================================================

---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 19 03:53PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a021f5a8443a0069

Hi Pengyao,

Thank you for your question about gene track updates for the dm3
assembly. There are two gene tracks on the dm3 assembly that are updated
on a regular basis. The RefSeq Genes track is update with new
information that we download from RefSeq on a nightly basis. The data
for the RefSeq Genes track was last updated 2014-09-13. The Ensembl
Genes track is updated whenever Ensembl releases a new version of their
gene predictions for the dm3 assembly. The data for the Ensembl Genes
track was last updated 2014-03-11. You can always see when the data in a
track was last updated by looking at a track's description page. You can
get to a track's description page by clicking the track name in the
groups below the main browser display, or by clicking the grey bar next
to the track on the far left of the main browser display. For example,
on the dm3 RefSeq Genes description page,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm3&g=refGene, you can see
the date just below the track settings on the line labeled "Data last
updated".

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 9/18/14, 12:07 PM, Pengyao Jiang wrote:

=============================================================================
Topic: Release 6 Drosophila melanogaster genome?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21d0fb05ff11cc47
=============================================================================

---------- 1 of 3 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 19 11:16AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/947ce4174dce3d3b

Hi Nelson,

Thank you for your question about updating the D. melanogaster assembly
in the UCSC Genome Browser. A preview of the BDGP Release 6/dm6 Genome
Browser is available on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=dm6. However, please
keep in mind that this our test server, and that much of the data has
not undergone our standard quality review process and is subject to
change. We do have plans to release this to our public website at
http://genome.ucsc.edu/, 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 9/18/14, 8:15 PM, Nelson Lau wrote:

---------- 2 of 3 ----------
From: Nelson Lau <***@brandeis.edu>
Date: Sep 19 02:41PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a040a59d93c1cfb6

Thanks, Matthew. Is the Liftover tool able to help us convert the
Dm3/Release5 coordinates to the Dm6/Release6 coordinates? We have a paper
accepted where the work was done on Dm3, but the journal would prefer all
the coordinates be adjusted to Dm6, including BED files. I understand this
build is on the test server, but presumably the new build will be released
soon? Please advise how we can convert all our file coordinates to Dm6.

*From:* Matthew Speir [mailto:***@soe.ucsc.edu]
*Sent:* Friday, September 19, 2014 2:16 PM
*To:* Nelson Lau; ***@soe.ucsc.edu
*Subject:* Re: [genome] Release 6 Drosophila melanogaster genome?

Hi Nelson,

Thank you for your question about updating the D. melanogaster assembly in
the UCSC Genome Browser. A preview of the BDGP Release 6/dm6 Genome Browser
is available on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=dm6. However, please
keep in mind that this our test server, and that much of the data has not
undergone our standard quality review process and is subject to change. We
do have plans to release this to our public website at
http://genome.ucsc.edu/, 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 9/18/14, 8:15 PM, Nelson Lau wrote:

Hello,

Do you have an ETA when the newest Release 6 of the Drosophila Melanogaster
genome will be loaded into the UCSC Browser? The current latest build is
Dm3, Release 5.

Thanks,

Nelson Lau, Ph.D.

Assistant Professor - Biology

Brandeis University

415 South St, MS029

Science Receiving

Waltham MA 02454, USA

Ph: 781-736-2445
http://www.bio.brandeis.edu/laulab

--

---------- 3 of 3 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 19 01:54PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4cd028f9b6834ceb

Hi Nelson,

Yes, you can use the liftOver tool just like you normally would to
convert dm3 to dm6 coordinates. You can access the web interface for
liftOver on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgLiftOver. To convert the
coordinates from dm3 to dm6 use the following settings:

Original Genome: D. melanogaster
Original Assembly: BDGP R5
New Genome: D. melanogaster
New Assembly: BDGP Release 6 + ISO1 MT

If you want to use the command line liftOver utility, you can find the
liftOver chain file on our preview downloads server here:
http://hgdownload-test.soe.ucsc.edu/goldenPath/dm3/liftOver/dm3ToDm6.over.chain.gz.
Again, please keep in mind that the data on our preview servers has yet
to undergo our standard quality assurance process and may be subject to
change.

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 9/19/14, 11:41 AM, Nelson Lau wrote:

=============================================================================
Topic: Question regarding the UCSC genome browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
=============================================================================

---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 19 12:20PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/247d8c94c5611406

Hello Nitika,

Thank you for your question about finding genes that match your probe sets.
I suggest that you start by building a custom track from your probe sets
and then use the "intersection" part of the UCSC Table Browser (
http://genome.ucsc.edu/cgi-bin/hgTables) to get the genes that overlap with
your probe sets. See
http://genome.ucsc.edu/goldenPath/help/customTrack.html for
more information about building a custom track, and
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection for
more information on using intersections in the Table Browser.

Depending on what gene information you need, the intersection tool might
not be enough for your research. If that is the case, the tools at Galaxy (
https://usegalaxy.org) can help you to get more specific gene information.
The following mailing list questions describe how to use the Table Browser
together with the tools at Galaxy to find gene information:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/LdYxhGwswno/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/lF0UpVKYi8I/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/y7zQDKO-8Hk/discussion

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

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