Digest for genome <at> soe.ucsc.edu - 5 updates in 4 topics
2014-07-21 17:23:24 GMT
- test vs regular liftover files [2 Updates]
- Bed to GTF file conversion [1 Update]
- Highly conserved miRNA families [1 Update]
- Custom track viewing restricted by genome assembly version for S.cerevisiae [1 Update]
Miriam Huntley <mhuntley <at> fas.harvard.edu> Jul 20 07:54PM -0400
Hi- I've noticed that some hg19 chain files that are missing from here
are posted on the test website
Is there a reason not to use these test files? Is there any documentation
for how valid these files are?
Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Jul 21 01:20PM -0400
The files located on our test server (
http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/liftOver/) have not yet
been reviewed by our quality assurance team. You are welcome to use these
files, however, please keep in mind our test server contains a lot of
experimental data and may undergo changes.
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
- - -
UCSC Genome Bioinformatics Group
On Sun, Jul 20, 2014 at 7:54 PM, Miriam Huntley <mhuntley <at> fas.harvard.edu>
meharji arumilli <mehar.com <at> gmail.com> Jul 21 07:09PM +0300
I tried using the following scripts to convert bed file to GTF file which
are available at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
*bedToGenePred input.bed stdout | genePredToGtf -utr file stdin output.gtf*
I have used the genePredToGtf script with -utr option to add 5UTR and 3UTR
features. However, the output doesn't have the UTR features in the final
GTF file irrespective of -utr option.
Could it be a bug in the script? Could someone give any ideas/suggestions
to achieve this.
"Igor Mett" <imett <at> quarkpharma.com> Jul 20 11:04AM +0300
Dear Sir or Madame,
I have got some predicted miRNA sites within my gene of interest in USCS
What does it mean: Highly conserved miRNA families?
Have I understood right that the predicted sites are conserved among
same gene of multiple vertebrates?
Thanks in advance,
Quark Pharmaceuticals Inc./QBI Enterprises Ltd.
QBI Enterprises Ltd.
Nes Ziona ISRAEL
Tel: +972 8 9305232
Fax +972 8 9406476
imett <at> quarkpharma.com <mailto:AAbramoff <at> quarkpharma.com>
The material in this transmission may contain confidential and/or
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the addressee, any disclosure or use of this information by you is
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"Rege, Mayuri" <Mayuri.Rege <at> umassmed.edu> Jul 19 11:37PM
I am having trouble viewing a bedGraph file in the Genome browser depending on the genome assembly version I use.
The older assembly (sacCer1) of the yeast genome is the only one that I can view the track with.
The error I get with the newer assemblies (sacCer2 and sacCer3) is Error Unrecognized format type=bedGraph line 2 of custom track
Here is the start file:
track type=bedGraph name=Histone
chr1 11604 11896 1.49203
The release log<https://genome.ucsc.edu/goldenPath/releaseLog.html> from UCSC lists all three assemblies as available. How can this be fixed? Thank you!
University of Massachusetts Medical School