g***@soe.ucsc.edu
2014-10-08 17:21:27 UTC
=============================================================================
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
- OMIM Genes [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/e531426941358ec4
- Transcriptional start site [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d192e896916d08bb
- request for overchain files [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c1d101cc95e2f243
- patients with deletions of a specfic gene. [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
- Menus on Genome Browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/eb940cb4d7101fe0
- Problem launching bam and vcf tracks via track hubs [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/11c475802ccc7dba
- ensGene table for bosTau7 [3 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a3c6cde58139d7e6
- Please help me with blastz-normalizelav [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/186e99a619e5fe5e
- Question about UCSC gene [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7932ede226b41a67
- phylop [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2cc5e627bd54aafa
- What happened to the paralogous region for PMS2? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c5d770a572a81ee2
- DNA sequence data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6e7ed5b952fd915b
- Question about viewing inter-chromosomal translocation [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2d25d317f8b93f0b
=============================================================================
Topic: OMIM Genes
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/e531426941358ec4
=============================================================================
---------- 1 of 1 ----------
From: Jason C Ting <***@lilly.com>
Date: Oct 08 05:06PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d64ca366a087e4d8
Dear UCSC Genome Browser,
How can I export the "OMIM Genes" track data?
In Table Browser, I can't find OMIM Genes track under the "Phenotype and Literature" group, nor under any other groups.
Thank you!
Jason C. Ting
Senior Research Scientist, LRL Resear IT Informatics
Eli Lilly and Company
Lilly Corporate Center, Indianapolis, IN 46285 USA
***@lilly.com
CONFIDENTIALITY NOTICE: This e-mail message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
=============================================================================
Topic: Transcriptional start site
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d192e896916d08bb
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 05:53PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/7380870054bb569f
Hello ruvalcabatrejo,
Thank you for your question about finding the transcriptional start site
and coding sequence for genes. Unfortunately your sample output is missing
from the question, so I can't advise you about those results.
If you would like to obtain the TSS and CDS start positions for a list of
genes, I suggest you use the UCSC Table Browser as follows. Here I will
assume that you want to obtain gene coordinates from the UCSC Genes track
of the human hg19 genome assembly.
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options
Clade: Mammals
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: UCSC Genes
Table: knownGene
Region: genome
Output format: selected fields from primary and related tables
Note: After you select the knownGene table, you can click the "describe
table schema" button to get a description of each of the different fields.
In particular, txStart contains the TSS coordinate, and cdsStart is the
start position of the CDS. These coordinates are 0-based (see
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms for more
information).
3. For "identifiers (names/accessions)", click "paste list" and paste your
list of genes into the text box that appears. Click "submit" when you are
done.
4. Click "get output".
5. On the next page, select the following options.
6. Click "get output"
You will be presented with data for each transcript of your matching genes.
Here is the output I got for the IL1RN gene:
#hg19.knownGene.name hg19.knownGene.txStart
hg19.knownGene.cdsStart hg19.kgXref.geneSymbol
uc002tix.1 113856936 113856936 IL1RN
uc002tiy.3 113875469 113885303 IL1RN
uc002tiz.3 113875469 113875595 IL1RN
uc002tja.3 113875469 113875595 IL1RN
uc002tjb.3 113885137 113885201 IL1RN
If you are interested in working further with the UCSC Table Browser and
related tools, I suggest you begin with the resources on our training page
at http://genome.ucsc.edu/training.html. The OpenHelix video tutorials in
particular offer a guided, example-driven introduction to our website.
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 Fri, Oct 3, 2014 at 8:51 AM, ruvalcabatrejo <***@gmail.com>
wrote:
---------- 2 of 2 ----------
From: ruvalcabatrejo <***@gmail.com>
Date: Oct 08 09:28AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/9770b91888852d89
Hi Jonathan,
Thank you so much for answering my question. I am curious why you used the
assembly Feb. 2009 (GRCh37/hg19) and not Dec.2013 (GRCh38/hg38)? When I use
assembly Dec.2013 (GRCh38/hg38) the output is closer to TSS that I already
have confirmed. Is assembly Feb. 2009 (GRCh37/hg19) more accurate and
trustworthy for TSSs? This is new to me so I am not very familiar with the
differences. I thought they were the same but the most recent assembly had
more accurate and recent information than previous assemblies.
This is the output I get with assembly Dec.2013 (GRCh38/hg38) for IL1RN:
#hg38.knownGene.name hg38.knownGene.txStart hg38.knownGene.cdsStart hg38.kgXref.geneSymbol
uc002tix.1 113099359 113099359 IL1RN
uc002tiy.3 113117892 113127726 IL1RN
uc002tiz.3 113117892 113118018 IL1RN
uc002tja.3 113117892 113118018 IL1RN
uc002tjb.3 113127560 113127624 IL1RN
Thank you for your time and help.
-Laura
On Tue, Oct 7, 2014 at 5:53 PM, Jonathan Casper <***@soe.ucsc.edu>
wrote:
=============================================================================
Topic: request for overchain files
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c1d101cc95e2f243
=============================================================================
---------- 1 of 1 ----------
From: jin jinpu <***@mail.cbi.pku.edu.cn>
Date: Oct 08 11:13PM +0800
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/5937d7c622ea8eb6
Dear Steve Heitner,
Thanks for the prompt reply last time. Now I meet another problem and could not find the overchain files
from human (hg19) to Gibbon (nomLeu3) in the ftp. It would be greatly appreciated if you could upload the
overchain files (hg19ToNomLeu3) to the ftp. Thanks very much.
Best,
Jinpu Jin
Peking University
=============================================================================
Topic: patients with deletions of a specfic gene.
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
=============================================================================
---------- 1 of 1 ----------
From: "Hasselt-2, P.M. van" <***@umcutrecht.nl>
Date: Oct 08 02:00PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/58981918bb918e66
Hi!
I have a question and hope you can be of help.: Only a minority of the deletions that we can find on your database have a clinical description. I was wondering whether it would be possible like to seek contact with clinicians who have a similar deletion. Since it is an x-linked problem, knowing the gender would already help a lot.
I hope you can tell me how to proceed!
Best regards, Peter van Hasselt pediatrician for inborn errors of metabolism.
------------------------------------------------------------------------------
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
------------------------------------------------------------------------------
This message may contain confidential information and is intended exclusively
for the addressee. If you receive this message unintentionally, please do not
use the contents but notify the sender immediately by return e-mail. University
Medical Center Utrecht is a legal person by public law and is registered at
the Chamber of Commerce for Midden-Nederland under no. 30244197.
Please consider the environment before printing this e-mail.
=============================================================================
Topic: Menus on Genome Browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/eb940cb4d7101fe0
=============================================================================
---------- 1 of 1 ----------
From: Martin Nicklin <***@sheffield.ac.uk>
Date: Oct 08 02:07PM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2cda985367a8e42b
I've noticed this before, that the menu options on the genome browser don't seem to be fully interactive. The group category (mammal, vertebrate, virus) doesn't update the actual species list. Today the problem became serious when out of interest (as an ex-virologist) I clicked on the Ebola genome option. this left me with no route back to looking at the human genome through the genome options. Selecting "mammal" rather than virus did not change the second menu. Selecting "vertebrate" cleared Ebola as an option, but did not allow me back to mammal, but allowed me into birds and fish. Selecting "mammal" again did not clear the list of non-mammalian vertebrate species. Shutting down Firefox and restarting does fix the problem, but it seems rather heavy handed. Is there a smoother fix?
Martin Nicklin
***@sheffield.ac.uk
Department of Infection and Immunity
Medical School
University of Sheffield [UK]
=============================================================================
Topic: Problem launching bam and vcf tracks via track hubs
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/11c475802ccc7dba
=============================================================================
---------- 1 of 2 ----------
From: Neethu Shah <***@gmail.com>
Date: Oct 07 04:55PM -0500
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f2005808383363e2
Hi,
This is to request info on the following.
This is a link to a hub URL:
http://genboree.org/REST/v1/grp/neethus_group/hub/BamVcf/hub.txt
There are two tracks : a bam and a Vcf Tabix data track, that are
being launched here.
This is the corresponding trackDb.txt
http://genboree.org/REST/v1/grp/neethus_group/hub/BamVcf/genome/hg19/trackDb.txt
track ALL_wgs_phase1_release_v3_20101123_snps_indels_sv_sites_vcf_gzZEfF2dZN
bigDataUrl http://genboree.org/REST/v1/grp/Examples%20and%20Test%20Data/db/CreateHub%20hg19%20-%20Example%20Data/fileData/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz
shortLabel ALL.wgs.phase1_re
longLabel FILE:ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz,
HOST:genboree.org, GROUP:Examples%20and%20Test%20Data,
DATABASE:CreateHub%20hg19%20-%20Example%20Data
type vcfTabix
track bam1_bamU5xwC2YR
bigDataUrl http://genboree.org/REST/v1/grp/Examples%20and%20Test%20Data/db/CreateHub%20hg19%20-%20Example%20Data/fileData/bam1.bam
shortLabel bam1.bam
longLabel FILE:bam1.bam, HOST:genboree.org,
GROUP:Examples%20and%20Test%20Data,
DATABASE:CreateHub%20hg19%20-%20Example%20Data
type bam
Custom upload of these tracks are working at the UCSC browser.
The problem is, that it fails to display the hub.
The utility tool that validates the hub - hubCheck, was run and it
completed successfully without any errors.
But once loaded the browser gives a message as "Hub Connect
Successful", "This hub not supported by UCSC". Please find the
attached screen shot.
Our nginx access log (in the same attachment) shows that the request
does not go beyond genomes.txt.
Please note that we encounter this problem only with bam and vcfTabix
data tracks.
Track hubs with bigWig and bigBed are successfully uploaded and displayed.
Could you please direct to what might be wrong here?
Thank you,
Neethu Shah
Genboree Team
Baylor College of Medicine
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 07:57PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2f94be9396fdfc35
Hello Neethu,
Thank you for your question about setting up a track hub for bam and vcf
files. We are having some trouble reproducing the problem - when we attempt
to load your track hub, it works just fine. The message that the hub is not
supported by UCSC is expected - it is a reminder for anyone who loads the
hub that UCSC did not create it, and that any questions about the hub data
should be sent to the creator.
When we load the hub, the bam and vcf tracks are set to "hide" by default.
They must be changed to a display level of "dense" or higher in the track
controls to see any data. Could that be the problem? If not, can you please
give a detailed description of something that your bigWig/bigBed hubs do
successfully, but that this hub does not?
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: ensGene table for bosTau7
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a3c6cde58139d7e6
=============================================================================
---------- 1 of 3 ----------
From: Chih Lee <***@engr.uconn.edu>
Date: Oct 07 03:01PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c9723b814cfa43f9
Hello,
Will this table be available for bosTau7 soon? Thanks.
I tried lifting over ensGene.txt from bosTau6 to bosTau7 but only 22,399
out of 26,740 records were lifted over successfully.
Best,
Chih Lee
---------- 2 of 3 ----------
From: Chih Lee <***@engr.uconn.edu>
Date: Oct 07 03:50PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4f9dff3943db1efb
It seems that the current Bos taurus assembly on Ensembl bosTau6 or UMD3.1.
That's probably why ensGene.txt is missing for bosTau7.
---------- 3 of 3 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 06:27PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/9a2863152845df01
Hello Chih,
Thank you for your question about the availability of the Ensembl genes
track for the bosTau7 genome assembly. As you noted, Ensembl is still using
the UMD3.1/bosTau6 version of the cow genome. Ensembl may be able to offer
more information about when they plan to move to the newer assembly; after
they do, then we can begin constructing this track for bosTau7.
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: Please help me with blastz-normalizelav
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/186e99a619e5fe5e
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 06:08PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1c246ff5bfa3f54c
Hello Jian,
Thank you for your question about the blastz-normalizeLav tool. We do not
have any documentation for this tool; one of our engineers believes that it
was written around 2002. The engineers goes on to offer that it is used to
"lift up" chunk coordinates into chromosome coordinates (or scaffold, etc.,
if the assembly has no chromosome sequences). It is similar to UCSC's
liftUp utility, except that it is specific to the lav format and lifts only
one chunk per invocation.
Another of our engineers points to the script blastz-run-ucsc, which uses
the blastz-normalizeLav tool as follows:
sub liftLav {
# Run blastz-normalizeLav to lift up chunk coords to sequence level.
my ($raw, $out, $tSeq, $qSeq) = @_;
my $tLen = $tSizes{$tSeq};
my $qLen = $qSeq ? $qSizes{$qSeq} : "0";
&run("blastz-normalizeLav $tLen $qLen < $raw > $out");
}
Here you can see that blastz-normalizeLav takes two length arguments and
reads the lav input file from standard input. Is that enough information to
get you started?
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: Question about UCSC gene
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7932ede226b41a67
=============================================================================
---------- 1 of 1 ----------
From: Seungjin Ryu <***@phd.einstein.yu.edu>
Date: Oct 07 07:39PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ad66a4fb98727fb8
Dear UCSC genome browser team,
Hello,
Actually, I have a question about UCSC gene isoform.
I am wondering how you find the UCSC gene isofrom which is not in refseq
gene.
For PRKCD human gene, there is an isoform, (uc003dgn.2) which is not in
refseq gene.
I want to know whether that isoform is really expressed in a cell or tissue
or not.
Please, let me know how to find the evidence.
Thank you for your help.
Best,
Seungjin
=============================================================================
Topic: phylop
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2cc5e627bd54aafa
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 03:03PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/da8aefe2b999d29d
Hello, Xin.
The phyloP table itself is not in BED format, so it is not possible to
obtain the table in BED12 format from the Table Browser. The table is in
BED-like format and if you would just like to obtain the entire table, you
can download it from http://hgdownload.cse.ucsc.edu/downloads.html. Select
the assembly of your choice, click the "Annotation database" link and
download the appropriate phyloP#way.txt.gz file.
Note that the table itself does not contain the actual scores. These are
contained in the wiggle file associated with the table. You could extract
the score data from the Table Browser using the "data points" option, but
you will be limited to 100,000 data points. You can get around this by
downloading the wiggle file and the hgWiggle utility. You can obtain the
wiggle file from http://hgdownload.cse.ucsc.edu/gbdb/. Select the assembly
of your choice, go to the multiz#way directory and download the
phyloP#way.wib file. The hgWiggle utility is available at
http://hgdownload.cse.ucsc.edu/admin/exe/. For assistance with hgWiggle,
you should refer to
http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database.
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
-----Original Message-----
From: Li, Xin [mailto:***@umassmed.edu]
Sent: Saturday, October 04, 2014 11:11 AM
To: ***@soe.ucsc.edu
Subject: [genome] phylop
Hello,
I am interested in using phlyop conservation scores, but the UCSC
has the limitation of 1,000 defined regions. Is there a way that I can run
regions more than that? The current phlyop conservation takes the first 3
columns in the bed files. Is there a way to look conservation for
transcripts in bed12 format?
Thank you.
Xin
--
=============================================================================
Topic: What happened to the paralogous region for PMS2?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c5d770a572a81ee2
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 11:20AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/85f08e25ce9fd04c
Hello, Vinayak.
The selfChain track could be missing alignments for a variety of reasons beyond our control. The best thing to do would be to extract the DNA sequence from your region of interest and blat it back to the genome to see what results it produces.
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: Vinayak Kulkarni [mailto:***@gmail.com]
Sent: Thursday, October 02, 2014 2:43 PM
To: ***@soe.ucsc.edu
Subject: [genome] What happened to the paralogous region for PMS2?
Dear USCS folks,
I was looking at PMS2 (NM_000535.5) and see a huge segment of duplicated region when looking at the self chain alignments in hg19. However when I move to GrCh38, that region disappears and I see only a very small intronic region in the self chain alignments track. Could you comment on what happened to the paralogous region?
Thank you very much,
Vinayak.
--
=============================================================================
Topic: DNA sequence data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6e7ed5b952fd915b
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 10:53AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/22c729814951d24
Hello, Linlin.
I don't believe you will find an official definition of how many Ns constitute a gap versus a number of consecutive ambiguous bases. If you view the hg38 Gap track description page, however (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gap), you will find gap statistics that show gaps as small as 10bp in length.
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
-----Original Message-----
From: ***@gmail.com [mailto:***@gmail.com] On Behalf Of Linlin Yan (???)
Sent: Monday, October 06, 2014 12:34 PM
To: ***@soe.ucsc.edu
Cc: Konstantinos Xylogiannopoulos; ***@soe.ucsc.edu
Subject: Re: [genome] DNA sequence data
Hi Steve,
I would like to ask a question following this thread. Since "a long string of Ns" typically represents a gap, is there a cut-off between ambiguous bases and size-undetermined gaps?
Best wishes!
---
Linlin Yan
PhD student
Peking University
=============================================================================
Topic: Question about viewing inter-chromosomal translocation
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2d25d317f8b93f0b
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 10:32AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e967c3b5f1c035c9
Hello, Moe.
This will work if you use BED format and the âurlâ option in your track line (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK). You can set the url to link to the ânameâ field of your BED data by using â$$â. This means for your chr1 data, the ânameâ field would be the chr11 coordinates. Based on the sample data you provided, your custom track would look like this:
track url=/cgi-bin/hgTracks?position=$$
chr1 69171674 69176128 chr11:6917167-6917612
chr11 6917167 6917612 chr1:69171674-69176128
If you wanted to include additional fields in your custom track, they would have to adhere to the BED standard (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
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: Mohammed Al Abri [mailto:***@cornell.edu]
Sent: Monday, October 06, 2014 12:48 PM
To: ***@soe.ucsc.edu
Subject: [genome] Question about viewing inter-chromosomal translocation
Hello UCSC team,
Thank you for making sure that ucsc browser is as awesome as it is.
I wanted to ask a question about the display interchromosomal translocations.
Basically, what I need to do is to link part of the translocation in one chromosome with its counterpart in another chromosome. Specifically, I want the user to be able to click on one part and get directed to the second. For example, if an interchromosomal translocation was between one chr1:2-500 and chr11:2-500, I wanted the user to be able to click on one to get directed to the other.
The closest format that I found to do what I want was the bedDetail format but that only displays the second part of the translocation in the ID field. I have attached the example I am using currently (in the horse genome).
I would really appreciate your help and advise on this issue.
Thank you
Moe
--
--
You received this digest because you're subscribed to updates for this group. You can change your settings on the group membership page:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/join
.
To unsubscribe from this group and stop receiving emails from it send an email to genome+***@soe.ucsc.edu.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+***@soe.ucsc.edu.
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
- OMIM Genes [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/e531426941358ec4
- Transcriptional start site [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d192e896916d08bb
- request for overchain files [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c1d101cc95e2f243
- patients with deletions of a specfic gene. [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
- Menus on Genome Browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/eb940cb4d7101fe0
- Problem launching bam and vcf tracks via track hubs [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/11c475802ccc7dba
- ensGene table for bosTau7 [3 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a3c6cde58139d7e6
- Please help me with blastz-normalizelav [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/186e99a619e5fe5e
- Question about UCSC gene [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7932ede226b41a67
- phylop [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2cc5e627bd54aafa
- What happened to the paralogous region for PMS2? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c5d770a572a81ee2
- DNA sequence data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6e7ed5b952fd915b
- Question about viewing inter-chromosomal translocation [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2d25d317f8b93f0b
=============================================================================
Topic: OMIM Genes
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/e531426941358ec4
=============================================================================
---------- 1 of 1 ----------
From: Jason C Ting <***@lilly.com>
Date: Oct 08 05:06PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d64ca366a087e4d8
Dear UCSC Genome Browser,
How can I export the "OMIM Genes" track data?
In Table Browser, I can't find OMIM Genes track under the "Phenotype and Literature" group, nor under any other groups.
Thank you!
Jason C. Ting
Senior Research Scientist, LRL Resear IT Informatics
Eli Lilly and Company
Lilly Corporate Center, Indianapolis, IN 46285 USA
***@lilly.com
CONFIDENTIALITY NOTICE: This e-mail message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
=============================================================================
Topic: Transcriptional start site
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d192e896916d08bb
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 05:53PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/7380870054bb569f
Hello ruvalcabatrejo,
Thank you for your question about finding the transcriptional start site
and coding sequence for genes. Unfortunately your sample output is missing
from the question, so I can't advise you about those results.
If you would like to obtain the TSS and CDS start positions for a list of
genes, I suggest you use the UCSC Table Browser as follows. Here I will
assume that you want to obtain gene coordinates from the UCSC Genes track
of the human hg19 genome assembly.
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options
Clade: Mammals
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: UCSC Genes
Table: knownGene
Region: genome
Output format: selected fields from primary and related tables
Note: After you select the knownGene table, you can click the "describe
table schema" button to get a description of each of the different fields.
In particular, txStart contains the TSS coordinate, and cdsStart is the
start position of the CDS. These coordinates are 0-based (see
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms for more
information).
3. For "identifiers (names/accessions)", click "paste list" and paste your
list of genes into the text box that appears. Click "submit" when you are
done.
4. Click "get output".
5. On the next page, select the following options.
From hg19.knownGene: name, txStart, cdsStart
From the linked hg19.kgXref table: geneSymbol6. Click "get output"
You will be presented with data for each transcript of your matching genes.
Here is the output I got for the IL1RN gene:
#hg19.knownGene.name hg19.knownGene.txStart
hg19.knownGene.cdsStart hg19.kgXref.geneSymbol
uc002tix.1 113856936 113856936 IL1RN
uc002tiy.3 113875469 113885303 IL1RN
uc002tiz.3 113875469 113875595 IL1RN
uc002tja.3 113875469 113875595 IL1RN
uc002tjb.3 113885137 113885201 IL1RN
If you are interested in working further with the UCSC Table Browser and
related tools, I suggest you begin with the resources on our training page
at http://genome.ucsc.edu/training.html. The OpenHelix video tutorials in
particular offer a guided, example-driven introduction to our website.
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 Fri, Oct 3, 2014 at 8:51 AM, ruvalcabatrejo <***@gmail.com>
wrote:
---------- 2 of 2 ----------
From: ruvalcabatrejo <***@gmail.com>
Date: Oct 08 09:28AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/9770b91888852d89
Hi Jonathan,
Thank you so much for answering my question. I am curious why you used the
assembly Feb. 2009 (GRCh37/hg19) and not Dec.2013 (GRCh38/hg38)? When I use
assembly Dec.2013 (GRCh38/hg38) the output is closer to TSS that I already
have confirmed. Is assembly Feb. 2009 (GRCh37/hg19) more accurate and
trustworthy for TSSs? This is new to me so I am not very familiar with the
differences. I thought they were the same but the most recent assembly had
more accurate and recent information than previous assemblies.
This is the output I get with assembly Dec.2013 (GRCh38/hg38) for IL1RN:
#hg38.knownGene.name hg38.knownGene.txStart hg38.knownGene.cdsStart hg38.kgXref.geneSymbol
uc002tix.1 113099359 113099359 IL1RN
uc002tiy.3 113117892 113127726 IL1RN
uc002tiz.3 113117892 113118018 IL1RN
uc002tja.3 113117892 113118018 IL1RN
uc002tjb.3 113127560 113127624 IL1RN
Thank you for your time and help.
-Laura
On Tue, Oct 7, 2014 at 5:53 PM, Jonathan Casper <***@soe.ucsc.edu>
wrote:
=============================================================================
Topic: request for overchain files
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c1d101cc95e2f243
=============================================================================
---------- 1 of 1 ----------
From: jin jinpu <***@mail.cbi.pku.edu.cn>
Date: Oct 08 11:13PM +0800
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/5937d7c622ea8eb6
Dear Steve Heitner,
Thanks for the prompt reply last time. Now I meet another problem and could not find the overchain files
from human (hg19) to Gibbon (nomLeu3) in the ftp. It would be greatly appreciated if you could upload the
overchain files (hg19ToNomLeu3) to the ftp. Thanks very much.
Best,
Jinpu Jin
Peking University
=============================================================================
Topic: patients with deletions of a specfic gene.
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
=============================================================================
---------- 1 of 1 ----------
From: "Hasselt-2, P.M. van" <***@umcutrecht.nl>
Date: Oct 08 02:00PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/58981918bb918e66
Hi!
I have a question and hope you can be of help.: Only a minority of the deletions that we can find on your database have a clinical description. I was wondering whether it would be possible like to seek contact with clinicians who have a similar deletion. Since it is an x-linked problem, knowing the gender would already help a lot.
I hope you can tell me how to proceed!
Best regards, Peter van Hasselt pediatrician for inborn errors of metabolism.
------------------------------------------------------------------------------
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
------------------------------------------------------------------------------
This message may contain confidential information and is intended exclusively
for the addressee. If you receive this message unintentionally, please do not
use the contents but notify the sender immediately by return e-mail. University
Medical Center Utrecht is a legal person by public law and is registered at
the Chamber of Commerce for Midden-Nederland under no. 30244197.
Please consider the environment before printing this e-mail.
=============================================================================
Topic: Menus on Genome Browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/eb940cb4d7101fe0
=============================================================================
---------- 1 of 1 ----------
From: Martin Nicklin <***@sheffield.ac.uk>
Date: Oct 08 02:07PM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2cda985367a8e42b
I've noticed this before, that the menu options on the genome browser don't seem to be fully interactive. The group category (mammal, vertebrate, virus) doesn't update the actual species list. Today the problem became serious when out of interest (as an ex-virologist) I clicked on the Ebola genome option. this left me with no route back to looking at the human genome through the genome options. Selecting "mammal" rather than virus did not change the second menu. Selecting "vertebrate" cleared Ebola as an option, but did not allow me back to mammal, but allowed me into birds and fish. Selecting "mammal" again did not clear the list of non-mammalian vertebrate species. Shutting down Firefox and restarting does fix the problem, but it seems rather heavy handed. Is there a smoother fix?
Martin Nicklin
***@sheffield.ac.uk
Department of Infection and Immunity
Medical School
University of Sheffield [UK]
=============================================================================
Topic: Problem launching bam and vcf tracks via track hubs
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/11c475802ccc7dba
=============================================================================
---------- 1 of 2 ----------
From: Neethu Shah <***@gmail.com>
Date: Oct 07 04:55PM -0500
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f2005808383363e2
Hi,
This is to request info on the following.
This is a link to a hub URL:
http://genboree.org/REST/v1/grp/neethus_group/hub/BamVcf/hub.txt
There are two tracks : a bam and a Vcf Tabix data track, that are
being launched here.
This is the corresponding trackDb.txt
http://genboree.org/REST/v1/grp/neethus_group/hub/BamVcf/genome/hg19/trackDb.txt
track ALL_wgs_phase1_release_v3_20101123_snps_indels_sv_sites_vcf_gzZEfF2dZN
bigDataUrl http://genboree.org/REST/v1/grp/Examples%20and%20Test%20Data/db/CreateHub%20hg19%20-%20Example%20Data/fileData/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz
shortLabel ALL.wgs.phase1_re
longLabel FILE:ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz,
HOST:genboree.org, GROUP:Examples%20and%20Test%20Data,
DATABASE:CreateHub%20hg19%20-%20Example%20Data
type vcfTabix
track bam1_bamU5xwC2YR
bigDataUrl http://genboree.org/REST/v1/grp/Examples%20and%20Test%20Data/db/CreateHub%20hg19%20-%20Example%20Data/fileData/bam1.bam
shortLabel bam1.bam
longLabel FILE:bam1.bam, HOST:genboree.org,
GROUP:Examples%20and%20Test%20Data,
DATABASE:CreateHub%20hg19%20-%20Example%20Data
type bam
Custom upload of these tracks are working at the UCSC browser.
The problem is, that it fails to display the hub.
The utility tool that validates the hub - hubCheck, was run and it
completed successfully without any errors.
But once loaded the browser gives a message as "Hub Connect
Successful", "This hub not supported by UCSC". Please find the
attached screen shot.
Our nginx access log (in the same attachment) shows that the request
does not go beyond genomes.txt.
Please note that we encounter this problem only with bam and vcfTabix
data tracks.
Track hubs with bigWig and bigBed are successfully uploaded and displayed.
Could you please direct to what might be wrong here?
Thank you,
Neethu Shah
Genboree Team
Baylor College of Medicine
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 07:57PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/2f94be9396fdfc35
Hello Neethu,
Thank you for your question about setting up a track hub for bam and vcf
files. We are having some trouble reproducing the problem - when we attempt
to load your track hub, it works just fine. The message that the hub is not
supported by UCSC is expected - it is a reminder for anyone who loads the
hub that UCSC did not create it, and that any questions about the hub data
should be sent to the creator.
When we load the hub, the bam and vcf tracks are set to "hide" by default.
They must be changed to a display level of "dense" or higher in the track
controls to see any data. Could that be the problem? If not, can you please
give a detailed description of something that your bigWig/bigBed hubs do
successfully, but that this hub does not?
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: ensGene table for bosTau7
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a3c6cde58139d7e6
=============================================================================
---------- 1 of 3 ----------
From: Chih Lee <***@engr.uconn.edu>
Date: Oct 07 03:01PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c9723b814cfa43f9
Hello,
Will this table be available for bosTau7 soon? Thanks.
I tried lifting over ensGene.txt from bosTau6 to bosTau7 but only 22,399
out of 26,740 records were lifted over successfully.
Best,
Chih Lee
---------- 2 of 3 ----------
From: Chih Lee <***@engr.uconn.edu>
Date: Oct 07 03:50PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4f9dff3943db1efb
It seems that the current Bos taurus assembly on Ensembl bosTau6 or UMD3.1.
That's probably why ensGene.txt is missing for bosTau7.
---------- 3 of 3 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 06:27PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/9a2863152845df01
Hello Chih,
Thank you for your question about the availability of the Ensembl genes
track for the bosTau7 genome assembly. As you noted, Ensembl is still using
the UMD3.1/bosTau6 version of the cow genome. Ensembl may be able to offer
more information about when they plan to move to the newer assembly; after
they do, then we can begin constructing this track for bosTau7.
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: Please help me with blastz-normalizelav
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/186e99a619e5fe5e
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Oct 07 06:08PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1c246ff5bfa3f54c
Hello Jian,
Thank you for your question about the blastz-normalizeLav tool. We do not
have any documentation for this tool; one of our engineers believes that it
was written around 2002. The engineers goes on to offer that it is used to
"lift up" chunk coordinates into chromosome coordinates (or scaffold, etc.,
if the assembly has no chromosome sequences). It is similar to UCSC's
liftUp utility, except that it is specific to the lav format and lifts only
one chunk per invocation.
Another of our engineers points to the script blastz-run-ucsc, which uses
the blastz-normalizeLav tool as follows:
sub liftLav {
# Run blastz-normalizeLav to lift up chunk coords to sequence level.
my ($raw, $out, $tSeq, $qSeq) = @_;
my $tLen = $tSizes{$tSeq};
my $qLen = $qSeq ? $qSizes{$qSeq} : "0";
&run("blastz-normalizeLav $tLen $qLen < $raw > $out");
}
Here you can see that blastz-normalizeLav takes two length arguments and
reads the lav input file from standard input. Is that enough information to
get you started?
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: Question about UCSC gene
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7932ede226b41a67
=============================================================================
---------- 1 of 1 ----------
From: Seungjin Ryu <***@phd.einstein.yu.edu>
Date: Oct 07 07:39PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ad66a4fb98727fb8
Dear UCSC genome browser team,
Hello,
Actually, I have a question about UCSC gene isoform.
I am wondering how you find the UCSC gene isofrom which is not in refseq
gene.
For PRKCD human gene, there is an isoform, (uc003dgn.2) which is not in
refseq gene.
I want to know whether that isoform is really expressed in a cell or tissue
or not.
Please, let me know how to find the evidence.
Thank you for your help.
Best,
Seungjin
=============================================================================
Topic: phylop
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2cc5e627bd54aafa
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 03:03PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/da8aefe2b999d29d
Hello, Xin.
The phyloP table itself is not in BED format, so it is not possible to
obtain the table in BED12 format from the Table Browser. The table is in
BED-like format and if you would just like to obtain the entire table, you
can download it from http://hgdownload.cse.ucsc.edu/downloads.html. Select
the assembly of your choice, click the "Annotation database" link and
download the appropriate phyloP#way.txt.gz file.
Note that the table itself does not contain the actual scores. These are
contained in the wiggle file associated with the table. You could extract
the score data from the Table Browser using the "data points" option, but
you will be limited to 100,000 data points. You can get around this by
downloading the wiggle file and the hgWiggle utility. You can obtain the
wiggle file from http://hgdownload.cse.ucsc.edu/gbdb/. Select the assembly
of your choice, go to the multiz#way directory and download the
phyloP#way.wib file. The hgWiggle utility is available at
http://hgdownload.cse.ucsc.edu/admin/exe/. For assistance with hgWiggle,
you should refer to
http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database.
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
-----Original Message-----
From: Li, Xin [mailto:***@umassmed.edu]
Sent: Saturday, October 04, 2014 11:11 AM
To: ***@soe.ucsc.edu
Subject: [genome] phylop
Hello,
I am interested in using phlyop conservation scores, but the UCSC
has the limitation of 1,000 defined regions. Is there a way that I can run
regions more than that? The current phlyop conservation takes the first 3
columns in the bed files. Is there a way to look conservation for
transcripts in bed12 format?
Thank you.
Xin
--
=============================================================================
Topic: What happened to the paralogous region for PMS2?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c5d770a572a81ee2
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 11:20AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/85f08e25ce9fd04c
Hello, Vinayak.
The selfChain track could be missing alignments for a variety of reasons beyond our control. The best thing to do would be to extract the DNA sequence from your region of interest and blat it back to the genome to see what results it produces.
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: Vinayak Kulkarni [mailto:***@gmail.com]
Sent: Thursday, October 02, 2014 2:43 PM
To: ***@soe.ucsc.edu
Subject: [genome] What happened to the paralogous region for PMS2?
Dear USCS folks,
I was looking at PMS2 (NM_000535.5) and see a huge segment of duplicated region when looking at the self chain alignments in hg19. However when I move to GrCh38, that region disappears and I see only a very small intronic region in the self chain alignments track. Could you comment on what happened to the paralogous region?
Thank you very much,
Vinayak.
--
=============================================================================
Topic: DNA sequence data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6e7ed5b952fd915b
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 10:53AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/22c729814951d24
Hello, Linlin.
I don't believe you will find an official definition of how many Ns constitute a gap versus a number of consecutive ambiguous bases. If you view the hg38 Gap track description page, however (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gap), you will find gap statistics that show gaps as small as 10bp in length.
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
-----Original Message-----
From: ***@gmail.com [mailto:***@gmail.com] On Behalf Of Linlin Yan (???)
Sent: Monday, October 06, 2014 12:34 PM
To: ***@soe.ucsc.edu
Cc: Konstantinos Xylogiannopoulos; ***@soe.ucsc.edu
Subject: Re: [genome] DNA sequence data
Hi Steve,
I would like to ask a question following this thread. Since "a long string of Ns" typically represents a gap, is there a cut-off between ambiguous bases and size-undetermined gaps?
Best wishes!
---
Linlin Yan
PhD student
Peking University
=============================================================================
Topic: Question about viewing inter-chromosomal translocation
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2d25d317f8b93f0b
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 07 10:32AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e967c3b5f1c035c9
Hello, Moe.
This will work if you use BED format and the âurlâ option in your track line (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK). You can set the url to link to the ânameâ field of your BED data by using â$$â. This means for your chr1 data, the ânameâ field would be the chr11 coordinates. Based on the sample data you provided, your custom track would look like this:
track url=/cgi-bin/hgTracks?position=$$
chr1 69171674 69176128 chr11:6917167-6917612
chr11 6917167 6917612 chr1:69171674-69176128
If you wanted to include additional fields in your custom track, they would have to adhere to the BED standard (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
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: Mohammed Al Abri [mailto:***@cornell.edu]
Sent: Monday, October 06, 2014 12:48 PM
To: ***@soe.ucsc.edu
Subject: [genome] Question about viewing inter-chromosomal translocation
Hello UCSC team,
Thank you for making sure that ucsc browser is as awesome as it is.
I wanted to ask a question about the display interchromosomal translocations.
Basically, what I need to do is to link part of the translocation in one chromosome with its counterpart in another chromosome. Specifically, I want the user to be able to click on one part and get directed to the second. For example, if an interchromosomal translocation was between one chr1:2-500 and chr11:2-500, I wanted the user to be able to click on one to get directed to the other.
The closest format that I found to do what I want was the bedDetail format but that only displays the second part of the translocation in the ID field. I have attached the example I am using currently (in the horse genome).
I would really appreciate your help and advise on this issue.
Thank you
Moe
--
--
You received this digest because you're subscribed to updates for this group. You can change your settings on the group membership page:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/join
.
To unsubscribe from this group and stop receiving emails from it send an email to genome+***@soe.ucsc.edu.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+***@soe.ucsc.edu.