genome | 29 Apr 19:12 2016

Digest for genome <at> soe.ucsc.edu - 4 updates in 3 topics

"Cellier, Mathieu" <Mathieu.Cellier <at> iaf.inrs.ca>: Apr 29 02:47AM

Hi there,
 
I have been working for a while with hg19 creating a series of sessions that I intend to use recurrently.
However a dataset of interest could not be uploaded in hg19 and the author kindly forwarded me a hg38 session.
Unfortunately, I tried to save it and this resulted in a loss of my hg19 sessions!
Is it possible to get back to my hg19 sessions? - I hope so very much!...
 
Thank you in advance for your help.
 
Best,
 
Mathieu Cellier
Brian Lee <brianlee <at> soe.ucsc.edu>: Apr 28 10:21PM -0700

Dear Mathieu,
 
Thank you for using the UCSC Genome Browser and creating sessions to share
your data. Please know that your session data still exists, I have done a
quick verification on an account matching the email you provided.
 
Can you please confirm that you are accessing http://genome.ucsc.edu/? And
not, for example, our European mirror at genome-euro.ucsc.edu or any other
mirror of the browser? Also, can you check and confirm that you are logged
in as yourself with the account matching your email?
 
Thank you again for your using the UCSC Genome Browser and sessions. 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 our
private list genome-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genomics Institute
 
On Thu, Apr 28, 2016 at 7:47 PM, Cellier, Mathieu <
Matthew Speir <mspeir <at> soe.ucsc.edu>: Apr 28 11:05AM -0700

Hi Kanwar,
 
Thank you for your question about obtaining miRNA annotations for hg19
from the UCSC Genome Browser.
 
You can obtain a BED file of miRNAs from the Table Browser using the
following steps:
 
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: GENCODE Genes V19
table: Basic (wgEncodeGencodeBasicV19)
output: BED - browser extensible data
output file: enter a file name to save your results to a file, or
leave blank to display results in your browser
 
3. Next to "filter", click "create".
4. Select the wgEncodeGencodeAttrsV19 from the "Linked Tables" section
5. Click "allow filtering using fields in checked tables".
6. Type "miRNA" in the "geneType" and "transciptType" fields of the
hg19.wgEncodeGencodeAttrsV19 based filters section.
The "geneType" line should read: geneType does match miRNA
The "transcriptType" line should read: transcriptType does
match miRNA
 
7. Click "Submit".
8. Click "get output".
9. Choose your BED output formatting options, and click "get BED".
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/27/16 3:37 PM, shamsher jagat wrote:
Matthew Speir <mspeir <at> soe.ucsc.edu>: Apr 28 10:27AM -0700

Hi Marjan,
 
Thank you for your question about gene names in the UCSC Genome Browser.
 
We import much of our data from other sources. If these external sources
still label the gene as "Zfos1", then that's what will be displayed in
our Genome Browser. For example, the RefSeq page,
https://www.ncbi.nlm.nih.gov/nuccore/NM_001081005?report=GenBank, still
includes "Zfos1" in its title "Mus musculus zinc finger, NFX1-type
containing 1, opposite strand RNA 1 (Zfos1), mRNA". It appears that this
is also the case for GENCODE/Ensembl:
http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000074578;r=2:167062934-167065862.
 
I would recommend contacting the groups generating these annotations and
recommend that they change this in their databases. Once that happens,
these changes will make their way into our databases as we import them.
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/27/16 4:45 PM, Marjan Askarian-Arimi wrote:
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genome | 26 Apr 19:27 2016

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

"Arumilli, Meharji" <meharji.arumilli <at> helsinki.fi>: Apr 26 05:02PM +0300

Dear all,
 
Could you help us to find the Segmental Duplications table to download
for canFam3.1 assembly? I would like to access the regions defined in
the link
(https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=genomicSuperDups)
for dog genome.
 
Br
Mehar
Brian Lee <brianlee <at> soe.ucsc.edu>: Apr 25 01:30PM -0700

Dear Simon,
 
Thank you for using the UCSC Genome Browser and the Track Hub feature and
your question regarding an error about unsupported type.
 
The error is arising from a line in your trackDb.txt where instead of "type
bam" there is some additional metadata that should be trimmed from "type
21814_accepted_hits.bam" to be only "type bam". That information might be
better placed in the "track uniqueTrackName" line such as "track
name_metadata", for example, "track uniqueTrackName_21814_accepted_hits".
While you suggest it was working previously, it should not have worked, for
more details see this trackDb statement link:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#commonSettings
 
If you change all these "type metadata.bam" lines to only be "type bam" it
should correct the issue. If it does not fix the issue, please respond with
more information.
 
curl -s "
http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/mm10/trackDb_out_mm10.txt"
| grep type
curl -s "
http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/mm9/trackDb_out_mm9.txt"
| grep type
 
 
Thank you again for your inquiry and using the UCSC Genome Browser. 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
togenome-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genomics Institute
 
On Fri, Apr 22, 2016 at 2:16 AM, HARDING Simon <simon.harding <at> igmm.ed.ac.uk>
wrote:
 
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genome | 25 Apr 19:19 2016

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Pirah Uqaili <uqaili_90 <at> hotmail.com>: Apr 25 10:27AM +0500

Hello,
I am a PhD scholar doing research in the field of Molecular Biology and Genetics.
I want to find STR marker of a particular gene.
How am I suposed to find it on your UCSC genome browser? Please guide me
 
 
 
Regards,Ms. Pirah Atif Uqaili,PhD Scholar,Molecular Biology and Genetics Dept.,Medical Research Center,LUMHS, Jamshoro
Nagarjun V <arjun53ster <at> gmail.com>: Apr 22 12:57PM -0400

Hi,
 
Could you please provide chain files for the liftOver utility to convert
 
1. Hg38 coordinates to Galgal4 (chicken)
2. Hg38 coordinates to Rnor 6 (Rattus Norvegicus)
 
They are not available at the download link here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/
 
Thanks and regards,
 
--
Nagarjun Vijay, PhD
 
Lab of Molecular and Genomic Evolution,
Department of Ecology and Evolutionary Biology,
College of Literature, Science, and the Arts
University of Michigan,
Ann Arbor, MI, USA
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genome | 22 Apr 19:11 2016

Digest for genome <at> soe.ucsc.edu - 5 updates in 5 topics

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Apr 22 09:33AM -0700

Hello Christie,
 
Thanks for your question. It's possible you are looking at the snp141Common
table on hg38 instead of hg19. If not, could you please provide a sample of
the genomic coordinates so we can take a closer look?
 
 
*If you have any further questions, please reply to genome <at> soe.ucsc.edu
<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 <genome-www <at> soe.ucsc.edu>.*
Regards,
Luvina
 
--
Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu
 
 
 
 
On Wed, Apr 13, 2016 at 6:51 AM, Christie Burton <
Matthew Speir <mspeir <at> soe.ucsc.edu>: Apr 22 08:55AM -0700

Hi Jane,
 
Thank you for your question about visualizing and obtaining sequence for
cDNAs in the UCSC Genome Browser.
 
Some tracks in the UCSC Genome Browser contain cDNA sequences, such as
the "mRNAs" tracks. For example, here is the description page for the
"Human mRNAs" track on the hg38/GRCh38 assembly of the human genome:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=mrna. Here you can
see this mRNAs track in the Genome Browser alongside the GENCODE v22
track for the SOD1 gene:
 
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_Sod1mRnaMlq
 
We just released a YouTube video that details how to obtain the sequence
for items in the track of your choice:
http://genome.ucsc.edu/training/vids/index.html#vid08. I would start at
time "5:40" in the video, which is where the steps describing how to get
sequence begin. While the video describes getting the sequence for items
in a different track, you can adapt the steps to your needs by selecting
"group: mRNA and EST", "track: Human mRNAs", and "table: all_mrna".
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/20/16 9:21 AM, Jane Bugler wrote:
HARDING Simon <simon.harding <at> igmm.ed.ac.uk>: Apr 22 09:16AM

Dear UCSC
 
We have a track hub set up for the GUDMAP project at
 
http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt
 
Until recently it has been functioning fine, but now we see this error when trying to load it.
 
ERROR: Unsupported type '13156_CM4G.bam' in hub http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt genome mm9 track 13156_CM4G
 
Running hubCheck gives:
 
./hubCheck.exe hub.txt
Found 2 problems:
Unsupported type '13156_CM4G.bam' in hub hub.txt genome mm9 track 13156_CM4G
Unsupported type '21814_accepted_hits.bam' in hub hub.txt genome mm10 track E14_5_DRG_(10ng,_high_volume)
 
 
The directories that hold those BAM files contain index (.bai) files and they are accessible. The site documentation still says BAM is supported. Can you advise on what might be happening here and how to resolve?
 
Many thanks
 
--
Simon D. Harding, PhD.
MRC HGU
MRC IGMM at University of Edinburgh
Crewe Road, EDINBURGH, EH4 2XU
 
 
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Zhenguo Zhang <zzhang65 <at> ur.rochester.edu>: Apr 21 04:52PM -0400

Dear UCSC Team:
 
My research now is using the genome alignments from your website, which
are very helpful. Thank you for having made them.
 
Since D. simulans has gotten much better updated genome sequence (see
the description and relevant links at
http://flybase.org/static_pages/feature/previous/articles/2015_02/Dsim_r2.01.html)
and most people in the Drosophila community may use the updated genome,
it will be fantastic if a new genome alignment between dm3 (D.
melanogaster) and the updated D. simulans genome can be made. Could you
please make this genome alignment or do you have plan to make it? Thanks.
 
Best regards!
 
Zhenguo
--
------------------------------------------------------------------------
Zhenguo Zhang, Ph.D
University of Rochester
Department of Biology
/River Campus Box 270211
Rochester, New York 14627-0211
Phone: (585) 276-2183; /
Email: z.zhang <at> rochester.edu or zhangz.sci <at> gmail.com
 
Home Page: http://molevol.altervista.org/
Lab page: http://blogs.rochester.edu/PresgravesLab/
Matthew Speir <mspeir <at> soe.ucsc.edu>: Apr 22 08:05AM -0700

Hi Chiara,
 
Thank you for your question about obtaining data for multiple tracks in
your saved sessions.
 
Unfortunately, we currently don't have a way to extract data for
multiple tracks in a saved session. You will likely have to use the
Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables, to extract the
data for each track in your session one at a time.
 
There is the Data Integrator,
http://genome.ucsc.edu/cgi-bin/hgIntegrator, that allows you to extract
data for multiple tracks at once based on intersections with another
track, but all of the data is concatenated into one file and one row can
contain data from multiple tracks based on the intersection. I'm not
sure how useful this tool would be in this case.
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/20/16 8:54 AM, Chiara Balestrieri wrote:
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genome | 21 Apr 19:22 2016

Digest for genome <at> soe.ucsc.edu - 8 updates in 7 topics

Christopher Lee <chmalee <at> ucsc.edu>: Apr 21 10:22AM -0700

Hi Laura,
 
Thank you for your question about missing gene names with RefSeq records.
We are a little unsure as to what gene names you are referring to, do you
mind sharing a couple example refSeq transcripts that are missing gene
names?
 
Thanks,
 
On Mon, Apr 18, 2016 at 3:35 PM, 'Laura Smith' via UCSC Genome Browser
Christopher Lee <chmalee <at> ucsc.edu>: Apr 21 10:21AM -0700

Hi Faravar,
 
Thank you for your question about ClinGen CNV nssv706353. If you click on
the
item in the browser, you will see the details page with with the line:
 
Variant type: copy_number_loss
 
which according to ClinGen is classified as pathogenic.
 
This publication describes the criteria for ClinGen CNV pathogenicity:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869000/
 
Thank you again for your inquiry and using the UCSC Genome Browser. 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.
 
On Fri, Apr 15, 2016 at 10:06 PM, 'faravar khordadpoor' via UCSC Genome
"Li, Aiguo (NIH/NCI) [E]" <liai <at> mail.nih.gov>: Apr 21 02:10PM

Dear all,
 
I created a track using the following syntax and it seems working well. However the description shows on the top of the display in the middle of the screen, but the name does not show on the left panel. Is there a way to show name in vcfTabix track type?
 
track type=vcfTabix name="827_CL_WGS" description="827 cell line WGS data" maxWindowToDraw=200000 db=hg19 visibility=pack bigDataUrl=http://helix.nih.gov/~NOB2/827CL.ucsc.vcf.gz
 
Thanks,
 
Anna
Matthew Speir <mspeir <at> soe.ucsc.edu>: Apr 20 10:40AM -0700

Hi Mark,
 
Thank you for your question about the knownToRefSeq table in the UCSC
Genome Browser.
 
The knownToRefSeq only associates IDs of items in the GENCODE v22 track
with those items they overlap in the RefSeq Genes track. In this case,
uc003haa.4 is a long transcript that overlaps a large region that
includes multiple other transcripts, meaning that all of those
transcripts will appear alongside it in the knownToRefSeq table. You can
see this if you look at uc003haa.4 in the Genome Browser with both the
GENCODE v22 and RefSeq Genes tracks:
 
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_uc003haa.4
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/18/16 9:51 PM, Mark Brown wrote:
Mark Brown <mbrown89 <at> gmail.com>: Apr 20 01:45PM -0700

Hi, Matthew
 
Thanks! I can see why uc003haa.4 is linked to NM_006206 now.
 
However, I have follow-up questions on how to obtain the best gene
structure for a RefSeq entry.
 
(1) It seem UCSC genome browser gateway search looksup RefSeq number using
to hg38.refGene table. E.g. for NM_006206
 
select name,chrom,strand,txStart,txEnd from hg38.refGene where
name='NM_006206'
name chrom strand txStart txEnd
0 NM_006206 chr4 + 54229096 *54298245*
 
NM_006206 is linked to uc003han.5 according to kgXref
select * from hg38.kgXref where mRNA='NM_006206'
kgID mRNA spID spDisplayID geneSymbol refseq \
0 uc003han.5 NM_006206 P16234 PGFRA_HUMAN PDGFRA NM_006206
 
However,
select name,chrom,strand,txStart,txEnd from hg38.knownGene where
name='uc003han.5'
name chrom strand txStart txEnd
0 uc003han.5 chr4 + 54229096 *54298247*
 
Now notice txEnd coordinates are different, comparing what obtained from
refGene and knownGene?
 
(2) Also it seems RefSeq entries do not always have corresponding UCSC
entries
E.g., I search NM_002929
I found two entries using
select name,chrom,strand,txStart,txEnd from hg38.refGene where
name='NM_002929'
name chrom strand txStart txEnd
0 NM_002929 chr13_KI270842v1_alt + 4330 8775
1 NM_002929 chr13 + 113667281 113735664
 
However, no entry in hg38.kgXref matches NM_002929. Two entries in
hg38.knownToRefSeq matches:
select name as UCSC, value as RefSeq from hg38.knownToRefSeq r where
value='NM_002929'
UCSC RefSeq
0 uc010tkf.3 NM_002929
1 uc058yoe.1 NM_002929
 
But neither of these two share the same gene structure with the two rows
returned by refGene:
select name,chrom,strand,txStart,txEnd from hg38.knownGene where name in
('uc058yoe.1','uc003han.5')
name chrom strand txStart txEnd
0 uc010tkf.3 chr13 + 113667154 113737735
1 uc058yoe.1 chr13 + 113726485 113735236
 
So my current understanding is: UCSC entries come from Ensembl. For a
given RefSeq number, if I trust NCBI's RefSeq gene structure, I should use
refGene table to retrieve the data. But if I trust transcripts from
Ensembl, I should map RefSeq into UCSC entries using kgXref first and
obtain gene structures from matched UCSC entries. If nothing found in
kgXref, I should use knownToRefSeq entry to find UCSC entries and obtain
gene structure that way. Is my understanding correct?
 
Thanks!
Erik Axelsson <erik.axelsson <at> imbim.uu.se>: Apr 20 09:39AM

Hi!
 
I've used the stand alone version of the LiftOver program to convert dog canfam3 coordinates to human hg38 coordinates. When I use the "In other genomes (convert)" tool under the "View" roll down menu on the UCSC canfam3 browser to test if my LiftOver results are consistent with those of the browser conversions ("In other genomes (convert)" ) I find that 3 out of 10 random tested SNPs map to a position 2 bases downstream of the position indicated by LiftOver. The remaining 7 SNPs map to the same position using both applications. I've tested several more SNPs and can confirm that this inconsistency is relatively common. I have used both the stand alone LiftOver tool and the UCSC batch conversion tool under the "Tools" roll down menu on the UCS C browser and the results of these two tools are always consistent indicating that my downstream handling of the stand alone LiftOver output is not causing the inconsistencies. Whenever I encounter an inconsistency between LiftOver and the "View/in other genomes (convert)" tool they appear both during conversion from canfam3 to hg19 and hg38 and the coordinates are always off by only 2 bases.
 
To give some examples of the inconsistencies I've attached an excel sheet comparing the results of the different conversion tools for 10 positions. For each position I have noted:
 
1. the original canfam3 position,
2. the hg38 position according to my stand alone LiftOver pipeline,
3. the hg38 position according to the UCSC browser LiftOver tool,
4. the hg38 position according to the "View/In other genomes(convert)" tool,
5. the hg19 position according to the UCSC browser LiftOver tool,
6. the hg19 position according to the "View/In other genomes(convert)" tool
 
The 3 inconsistent SNPs are marked in red.
 
Have you noticed a similar problem before? What do you think is wrong?
 
Thanks in advance!
 
Best wishes,
Erik
Jane Bugler <j.bugler.1 <at> research.gla.ac.uk>: Apr 20 05:21PM +0100

To whom it may concern ,
 
I am inquiring about how best to visualise and get the sequence of cDNA on the USCS genome browser. If there are any tutorials, they would also be most appreciated.
Kindest regards,
 
Jane
 
------------------------
Ms Jane Bugler
PhD Candidate
Institute of Cancer Sciences
Wolfson Wohl Cancer Research Centre
University of Glasgow
Garscube Estate
Switchback Road
Glasgow, G61 1QH
Chiara Balestrieri <balestrieri.c <at> gmail.com>: Apr 20 05:54PM +0200

Hi,
I'm Chiara and I work at IEO in Milan.
I have a problem with our internal database and for this reason I have a
special request.
In particular, I need for each my session to download all information
related on tracks.
 
I know that I can use this option "Save current settings to a local file",
but from this file I cannot obtain the url that I would use to rebuild the
DB.
 
Can you help me with this crazy problem?
 
Thank you
Chiara Balestrieri
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genome | 18 Apr 19:13 2016

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

"Pedro Manuel Martínez García" <pedro.martinez <at> cabimer.es>: Apr 18 12:46PM +0200

To Whom It May Concern,
 
As indicated in the website http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/, I am writing to gently ask for the LiftOver associated file hg18ToHg19.over.chain.
 
Thanks in advance.
 
Kind Regards,
 
Pedro.
faravar khordadpoor <faravarkhordadpoor <at> yahoo.com>: Apr 16 05:06AM

Dear sir,
 
 
 
This is to ask you about the ClinGenCNVs: (nssv706353). while the origin of this CNV is paternal how could it bepathogenic?
 
 
 
 
 
I would highly appreciate if youexplain in this case.
 
 
 
 
 
Best Regards,
 
Dr. faravar Khordadpoor
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genome | 15 Apr 19:25 2016

Digest for genome <at> soe.ucsc.edu - 3 updates in 3 topics

"Li, Aiguo (NIH/NCI) [E]" <liai <at> mail.nih.gov>: Apr 14 06:58PM

Dear all,
 
I assumed that in genome view the longer bar of a given gene indicates 3' end and short bar indicates 5' end. However, the attached CDKN2A gene has longer bars in both ends. Could you please help me to figure out which is the 5' and 3' of of this gene?
 
Thanks,
 
Anna
Thibaut Hourlier <th3 <at> sanger.ac.uk>: Apr 14 06:16PM +0100

Dear Meenakshi,
For some species like hedgehog for which the assembly was of low coverage and fragmented, Ensembl did a Projection build. This means that the hedgehog assembly was aligned to the human genome. Then the annotation was done on the result of the alignment. This allowed the creation of less fragmented genes but it joined scaffolds which were not joined in the original assembly. These are the GeneScaffold you can see in Ensembl. You can find a better explanation here: http://www.ensembl.org/info/genome/genebuild/2x_genomes.html.
UCSC seem to have kept the original assembly, this is why the gene is on multiple scaffolds.
 
Depending on the analysis you want to do you may want to download the data from the Ensembl FTP.
 
Regards
Thibaut
 
 
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Christopher Lee <chmalee <at> ucsc.edu>: Apr 14 10:15AM -0700

Hi Shicheng,
 
Thank you for your question about an error while loading custom tracks from
your
FTP server. You are seeing this error because you are trying to load too
many files
at once, and your FTP server is hitting its connection limit.
 
If you instead moved the files to an HTTP server, ideally one without limits
on the number of simultaneous connections allowed, you should be able to
load
your tracks just fine.
 
Thank you again for your inquiry and using the UCSC Genome Browser.
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.
 
On Mon, Apr 11, 2016 at 9:24 AM, Shicheng Guo <guoshicheng2005 <at> yeah.net>
wrote:
 
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genome | 14 Apr 19:06 2016

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

Eduardo Eyras <eduardo.eyras <at> upf.edu>: Apr 14 12:49PM +0200

Dear all,
 
extracting the Ensembl gene annotation from the Table Browser in GTF format
gives the transcript ID in both the gene and transcript fields of the 9th
column, e.g.:
 
gene_id "ENST00000492095"; transcript_id "ENST00000492095";
 
This is also so for other annotations like RefSeq or UCSC.
 
This GTF format makes only sense if the gene information is used.
 
I was wondering whether this is a bug in the system, or something
actually more difficult to solve.
 
in the meantime, we have written code to cluster transcripts into genes
from these GTFs, following the Ensembl genebuild code.
 
Please let me know whether this is something eventually fixable.
 
Thanks for the great work
best
 
Eduardo
 
--
Dr E Eyras
 
ICREA Research Professor
Universitat Pompeu Fabra
PRBB, Dr Aiguader 88 Tel: +34 93 316 0502 (ext 1502)
E08003 Barcelona, Spain Fax: +34 93 316 0550
 
http://scholar.google.com/citations?user=LiojlGoAAAAJ
http://www.researcherid.com/rid/L-1053-2014
http://regulatorygenomics.upf.edu/
Yecheng Huang <yhuang <at> uga.edu>: Apr 14 03:43PM

Matthew,
 
 
Thanks for the detailed response. My original gtf file is about 800MB. I am working on converting to bed then bigBed.
 
 
Another way is to trim the custom annotation to downsize the file size.
 
 
I will work this out and greatly appreciate your help.
 
 
Kind regards,
 
 
Yecheng Huang
 
EITS Georgia Advanced Computing Resource Center (GACRC)
University of Georgia
 
http://www.gacrc.uga.edu<http://www.rcc.uga.edu>
706-542-9071
 
 
 
________________________________
From: Matthew Speir <mspeir <at> soe.ucsc.edu>
Sent: Wednesday, April 13, 2016 11:52 AM
To: Yecheng Huang; genome <at> soe.ucsc.edu
Subject: Re: [genome] custom track uploading problem
 
Hi Yecheng,
 
Thank you for your question about uploading custom tracks to the UCSC Genome Browser.
 
That file is far too large to loaded in a plain-text custom track format, such as GTF or BED.
 
Annotation files of this size should be converted into one of our compressed, binary formats, such as bigBed or bigGenePred. These formats are placed on a publicly-accessible web server and the URL to this location is supplied to the UCSC Genome Browser. The Genome Browser will then request the information it needs from the file as needed for only the regions of the genome you are currently viewing. You can read more about the bigBed format here: http://genome.ucsc.edu/goldenPath/help/bigBed.html, and more about the bigGenePred format here: http://genome.ucsc.edu/goldenPath/help/bigGenePred.html. Both of these pages describe the formats themselves as well a s provide some information for converting your plain-text file into one of these formats using the command-line utilities we provide.
 
I should note that there is no "bigGTF" format and that you will need to convert your GTF file into either a BED or a genePred format before converting into one of the "big" formats. We provide the utilities gtfToGenePred and genePredToBed for converting your file between all of these different formats. You can find these two utilities and more on our downloads server here: http://hgdownload.soe.ucsc.edu/admin/exe/.
 
I hope this is helpful. If you have any further questions, please reply to genome <at> soe.ucsc.edu<mailto:genome <at> 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-www <at> soe.ucsc.edu<mailto:genome-www <at> soe.ucsc.edu>.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 4/12/16 10:34 AM, Yecheng Huang wrote:
 
 
Hi,
 
 
I use your Genome browser for my Dog assembly and annotation. This is a very great tool, thanks for the work.
 
 
When I tried to upload my own gtf file, I got this error:
 
needMem: trying to allocate 501484873 bytes (limit: 500000000)
 
 
The uploading file is about 800 MB, 120,000 transcripts. I take a subset ( 8000 transcript) to upload, it works.
 
 
Please advise any solutions.
 
 
Thanks a lot,
 
Yecheng Huang
 
EITS Georgia Advanced Computing Resource Center (GACRC)
University of Georgia
 
http://www.gacrc.uga.edu<http://www.rcc.uga.edu>
706-542-9071
 
--
Vince Forgetta <forgetta <at> gmail.com>: Apr 13 02:33PM -0400

Hi,
 
Is there a method and usage policy on how to programmatically access the
UCSC Genome Browser to generate browser images?
 
I would like to embed PNG images of the UCSC Genome Browser with plots I am
generating. I was thinking along the lines of somehow using browser lines
to specify the genome position and layout of tracks and submit this via URL
or some other method to UCSC Browser.
 
Thanks,
 
Vince
Christopher Lee <chmalee <at> ucsc.edu>: Apr 13 11:37AM -0700

Hi Louis,
 
Thank you for your question about the meaning of the "=" in the
conservation track.
For a description of the various symbols used in the conservation track
please see
the following page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr9&g=cons100way#TRACK_HTML
 
If you scroll down to the section titled "Display Conventions and
Configurations"
and find the sub-section "Gap Annotation", you will find the explanation
for the
double line:
 
"Double line: Aligning species has one or more unalignable bases in the gap
region.
Possibly due to excessive evolutionary distance between species or
independent indels
in the region between the aligned blocks in both species. "
 
Thank you again for your inquiry and using the UCSC Genome Browser.
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.
 
On Mon, Apr 11, 2016 at 8:51 AM, Louis Viollet <louis.viollet <at> gmail.com>
wrote:
 
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genome | 5 Apr 19:21 2016

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

"Hao, Shuanglin" <SHao <at> med.miami.edu>: Apr 05 03:03PM

Dear UCSC Genome Informatics Group
 
I would like to use your website to seek gene TSS and predict the gene promoters.
Could you please let me know the information?
 
Thank you very much.
Sincerely,
 
Shuanglin Hao, PhD,
 
Associate Professor &
Director of Preclinical and Basic Research
Department of Anesthesiology,
University of Miami Miller School of Medicine
1550 NW 10th Ave, Fox BLDG, Rm 304C
Miami, FL33136
Tel: 305-243-6420 (O)
305-243-8416 (L)
Fax: 305-243-9160 (O)
 
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"Timms, Andrew" <Andrew.Timms <at> seattlechildrens.org>: Apr 04 08:31PM

Hello,
 
I'm trying to line up a few pac bio reads to the zebrafish genome using blat.
 
When using the webbased blat I get a result such as (with many more):
 
 
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:59352014-59358576&db=danRer10&ss=../trash/hgSs/hgSs_genome_77d0_2c4040.pslx+../trash/hgSs/hgSs_genome_77d0_2c4040.fa&hgsid=488326591_I7jWKXDd0H1K6RJwvJtnmI8TlffO> details<http://genome.ucsc.edu/cgi-bin/hgc?o=59352013&g=htcUserAli&i=../trash/hgS s/hgSs_genome_77d0_2c4040.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_77d0_2c4040.fa+YourSeq&c=chr6&l=59352013&r=59358576&db=danRer10&hgsid=488326591_I7jWKXDd0H1K6RJwvJtnmI8TlffO> YourSeq 3255 251 7720 8024 92.2% 6 + 59352014 59358576 6563
 
 
Which makes a lot of sense, however when I try to do this on by standalone version I end up with lots and lots of smaller hits, the largest having ~1100 matches in a different region.
 
 
I've tried following the guidelines, https://genome.ucsc.edu/FAQ/FAQblat.html#blat5, but unfortunately that doesn't help.
 
 
Thanks for your time.
 
Andrew
 
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Gert Hulselmans <gert.hulselmans <at> med.kuleuven.be>: Apr 05 02:37PM +0200

Hi,
 
It would be nice if bigWigToBedGraph (and for consistency bigWigToWig)
would support BED as interval input instead of only allowing -chrom,
-start, -end.
 
Now I need to run bigWigToBedGraph 20000 times to get all regions.
 
$ bigWigToBedGraph
bigWigToBedGraph - Convert from bigWig to bedGraph format.
usage:
bigWigToBedGraph in.bigWig out.bedGraph
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
 
$ bigWigToWig
bigWigToWig - Convert bigWig to wig. This will keep more of the same
structure of the
original wig than bigWigToBedGraph does, but still will break up large
stepped sections
into smaller ones.
usage:
bigWigToWig in.bigWig out.wig
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
 
 
Thanks,
Gert
Christopher Lee <chmalee <at> ucsc.edu>: Apr 04 10:18AM -0700

Hi BW,
 
Thank you for your question about the meaning of the columns of your psl
file.
For a complete description of the psl file format please see the following
page:
http://genome.ucsc.edu/FAQ/FAQformat.html#format2
 
In the future please note that you can search our mailing list archives to
see if
your question has already been answered:
https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome
 
Thank you again for your inquiry and using the UCSC Genome Browser.
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.
 
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genome | 31 Mar 19:11 2016

Digest for genome <at> soe.ucsc.edu - 11 updates in 8 topics

Chirag Nepal <nepalchirag116 <at> gmail.com>: Mar 31 11:00AM +0200

Dear UCSC team,
 
I was looking for Spotted Gar genome assembly on UCSC download section, but did not find it.
Could you please point out the location if UCSC has the genome assembly data.
 
Thank you !
 
 
 
Cheers
Chirag Nepal, Ph.D
======================================
 
Post Doctoral Researcher, Andersen Group
http://www.bric.ku.dk/Research/andersen-group/ <http://www.bric.ku.dk/Research/andersen-group/>
Biotech Research and Innovation Centre
University of Copenhagen, Denmark
 
https://www.researchgate.net/profile/Chirag_Nepal2 <https://www.researchgate.net/profile/Chirag_Nepal2>
http://scholar.google.co.uk/citations?hl=en&user=ejoHmZQAAAAJ <http://scholar.google.co.uk/citations?hl=en&user=ejoHmZQAAAAJ>
https://twitter.com/ChiragNepal <https://twitter.com/ChiragNepal>
"Steve Heitner" <steve <at> soe.ucsc.edu>: Mar 31 09:48AM -0700

Hello, Chirag.
 
We do have the Spotted Gar assembly on our preview server (http://genome-preview.ucsc.edu/cgi-bin/hgGateway? <http://genome-preview.ucsc.edu/cgi-bin/hgGateway?&db=lepOcu1> &db=lepOcu1), but assemblies that are still under development do not typically have download files available as do assemblies on our public site. As our grant specifies that we focus on mammalian genomes, it is unlikely that the Spotted Gar assembly will be released to our public site any time soon, if at all.
 
That being said, if you are just looking for raw assembly data, you can get it directly from NCBI. See http://www.ncbi.nlm.nih.gov/assembly/GCF_000242695.1/ and ftp://ftp.ncbi.nlm.nih.gov/genomes/Lepisosteus_oculatus/.
 
Please contact us again at genome <at> soe.ucsc.edu <mailto:genome <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-www <at> soe.ucsc.edu <mailto:genome-www <at> soe.ucsc.edu> .
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 
 
 
From: Chirag Nepal [mailto:nepalchirag116 <at> gmail.com]
Sent: Thursday, March 31, 2016 2:01 AM
To: genome <at> soe.ucsc.edu
Subject: [genome] Spotted gar genome assembly on UCSC
 

 
Dear UCSC team,
 

 
I was looking for Spotted Gar genome assembly on UCSC download section, but did not find it.
 
Could you please point out the location if UCSC has the genome assembly data.
 

 
Thank you !
 

 

 

 
Cheers
 
Chirag Nepal, Ph.D
 
======================================
 
 
 
 
 
Post Doctoral Researcher, Andersen Group
 
http://www.bric.ku.dk/Research/andersen-group/
 
Biotech Research and Innovation Centre
 
University of Copenhagen, Denmark
 
 
https://www.researchgate.net/profile/Chirag_Nepal2
 
http://scholar.google.co.uk/citations?hl=en <http://scholar.google.co.uk/citations?hl=en&user=ejoHmZQAAAAJ> &user=ejoHmZQAAAAJ
 
https://twitter.com/ChiragNepal
 

 
--
Christopher Lee <chmalee <at> ucsc.edu>: Mar 31 09:32AM -0700

Hi Shao,
 
Thank you for your question about overlapping gaps in lower level net
alignments.
Could you provide us with the command lines used to extract the axt blocks,
as well
as a paste of a small region of the overlapping blocks you are seeing?
 
You can send this information directly to me if you do not wish to share
it with the public list.
 
Thank you again for your inquiry and using the UCSC Genome Browser.
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.
 
"Dong, Xianjun" <XDONG <at> RICS.BWH.HARVARD.EDU>: Mar 31 02:25PM

hi
 
I got this error when zooming out the region. Do you have any clue what it is for?
 
Warning/Error(s):
 
* Couldn't connect to database hgcentral on hgnfs1 as hgcentuser. Too many connections
 
Best
-Xianjun
 
 
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Christopher Lee <chmalee <at> ucsc.edu>: Mar 30 03:25PM -0700

Hi Ricardo,
 
Thank you for your question about missing telomere elements in the mm8 and
mm9 gap tables.
Our gap tables only contain data from the NCBI public build, and thus if
mm8 and mm9 have
no information about telomeres in their gap tables, it is because NCBI did
not annotate it
in their release.
 
We recommend using the mm10 data as it is the most recent mouse assembly
released, and
thus contains the most up to date and accurate information.
 
You may also try contacting the NCBI help desk,
https://www.ncbi.nlm.nih.gov/home/about/contact.shtml,
about updating this information on their site.
 
Thank you again for your inquiry and using the UCSC Genome Browser.
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.
 
On Thu, Mar 24, 2016 at 7:03 PM, Ricardo A. Verdugo <raverdugo <at> u.uchile.cl>
wrote:
 
Jorge Fernandez de Cossio <jorge.cossio <at> cigb.edu.cu>: Mar 30 09:23PM

Dear Greg Roe,
 
I will appreciate any related to:
 
I tried LiftOver TCGA aml data genome version 36 to version 37.
I created the BED tab delimited file like the below with the chr, StartPos and EndPos from the maf file, and pasted in the data and submitted.
chr3 127396114 127396115
chr3 127396114 127396115
chr15 86262345 86262351
chr4 36149165 36149168
chr6 129950550 129950553
chr20 31023271 31023272
chr2 25967233 25967234
chr12 14619468 14619471
chr5 40981538 40981540
...
...
The output was:
Successfully converted 220 records
Conversion failed on 2324 records
Almost all of the type #Deleted in new
 
Is there something wrong? Can I hope to use all these important project data remapped to updated genomes?
Thank you in advance for help
 
Best regards, -jorge
 
Jorge Fernandez de Cossio
Center for Genetic Engineering and Biotechnology
Cuba
 
 
 
 
************************************************************************
CIGB, Inaugurado el 1ro de julio de 1986 por Fidel. 30 A?os de apuestas por la vida.
************************************************************************
Matthew Speir <mspeir <at> soe.ucsc.edu>: Mar 30 11:53AM -0700

Hi Patrick,
 
Thank you for your question about accessing the hg19 assembly in the
UCSC Genome Browser.
 
Unfortunately, I'm unable to replicate this issue. The hg19 assembly
appears to be loading fine on our end. Can you confirm that you are
using our main site, http://genome.ucsc.edu/, or our official European
mirror, http://genome-euro.ucsc.edu/?
 
I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 3/30/16 9:10 AM, Patrick R Gonzales wrote:
Patrick R Gonzales <prgonzal <at> uab.edu>: Mar 30 06:55PM

Hello, Matthew:
 
The issue appears to have resolved itself.
 
Thanks for the prompt reply.
 
Best,
 
Pat
 
From: Matthew Speir [mailto:mspeir <at> soe.ucsc.edu]
Sent: Wednesday, March 30, 2016 1:53 PM
To: Patrick R Gonzales <prgonzal <at> uab.edu>; 'genome <at> soe.ucsc.edu' <genome <at> soe.ucsc.edu>
Subject: Re: [genome] UCSC browser Human hg19 not loading
 
Hi Patrick,
 
Thank you for your question about accessing the hg19 assembly in the UCSC Genome Browser.
 
Unfortunately, I'm unable to replicate this issue. The hg19 assembly appears to be loading fine on our end. Can you confirm that you are using our main site, http://genome.ucsc.edu/, or our official European mirror, http://genome-euro.ucsc.edu/?
 
I hope this is helpful. If you have any further questions, please reply to genome <at> soe.ucsc.edu<mailto:genome <at> 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-www <at> soe.ucsc.edu<mailto:genome-www <at> soe.ucsc.edu>.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
On 3/30/16 9:10 AM, Patrick R Gonzales wrote:
Hello:
 
The UCSC browser for the Human hg19 build has not been loading since yesterday afternoon. Help, please?
 
Pat
 
Patrick R. Gonzales, Ph.D., CG(ASCP)CM
 
ABMGG Clinical Cytogenetics Fellow
 
Cytogenetics Laboratory
Department of Genetics
The University of Alabama at Birmingham
720 20th Street S, Kaul Genetics Building
Birmingham, AL 35233-2032
 
205-996-2347
prgonzal <at> uab.edu<mailto:prgonzal <at> uab.edu>
https://www.uab.edu/medicine/genetics/clinical-laboratories/cytogenetics-laboratory
 
--
Matthew Speir <mspeir <at> soe.ucsc.edu>: Mar 30 11:58AM -0700

Hi Patrick,
 
I'm glad that the issue has resolved itself. Please contact us again if
you run into any more issues when using the UCSC Genome Browser.
 
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
Google Groups forum. If your question includes sensitive data, you may
send it instead to genome-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 3/30/16 11:55 AM, Patrick R Gonzales wrote:
"White, Jason" <jwhite <at> mytu.tuskegee.edu>: Mar 30 11:59AM -0500

Good Morning,
 
I am interested in identifying transcription factor binding sites on
miRNAs. With that said, I would like to speak with someone regarding the
Chip-seq data displayed on the genome browser. Specifically, I would like
to correlate the samples used to acquire the chip-seq data to my target
samples (prostate cancer). Additionally, I would like to know if the raw
data and experimental details are publicly available? Thanks!
 
--
Jason White
RCMI Core Lab Manager
Tuskegee University
RCMI/CBR
Room 2011-Williams-Bowie Hall
1200 West Montgomery Road
Tuskegee, Alabama 36088
Office: 334-727-8287
Fax: 334-724-4700
"J. C. Szamosi" <jc.szamosi <at> alumni.utoronto.ca>: Mar 30 01:36PM -0400

Hello all,
 
I downloaded the human rRNA track following the instructions here:
https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/rrna/genome/0X06cAZgHjU/YekSLOG7CQAJ
 
And did the same for mouse following similar instructions. In both cases,
the gtf files that I downloaded are annotating a large number of very small
sequences (50 - 150bp in length). I find this very surprising. Are the
whole rRNA regions not annotated as full, long sequences? The short
sequences in the gtf file aren't even contiguous, so it doesn't even cover
a long rRNA sequence as I would expect.
 
I'm hoping to use the gtf file to generate a fasta file of all the rRNA
sequences from the genome, but right now this isn't working. Am I missing
something?
 
Thanks
 
Jake
--
J. C. Szamosi, M.Sc.
Bioinformatician
Farncombe Metagenomics Facility
McMaster University
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genome | 30 Mar 19:06 2016

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

Patrick R Gonzales <prgonzal <at> uab.edu>: Mar 30 04:10PM

Hello:
 
The UCSC browser for the Human hg19 build has not been loading since yesterday afternoon. Help, please?
 
Pat
 
Patrick R. Gonzales, Ph.D., CG(ASCP)CM
 
ABMGG Clinical Cytogenetics Fellow
 
Cytogenetics Laboratory
Department of Genetics
The University of Alabama at Birmingham
720 20th Street S, Kaul Genetics Building
Birmingham, AL 35233-2032
 
205-996-2347
prgonzal <at> uab.edu<mailto:prgonzal <at> uab.edu>
https://www.uab.edu/medicine/genetics/clinical-laboratories/cytogenetics-laboratory
"Mutangadura, Tendai" <tendai <at> missouri.edu>: Mar 30 03:12PM

UCSC Help Desk Team
 
Could you please explain to me or show me a quick way of downloading sequence surrounding a coordinate or SNP of interest (dog reference) for a list of SNPs without doing this one SNP/sequence at a time?
 
Thank you,
-Tendai
Albert Vilella <albert.vilella <at> cegx.co.uk>: Mar 30 01:34PM +0100

Hi,
 
I would like to obtain a list of 50bp windows that are conserved in the
mammals multiple alignments. Something like a bed file where the name
column is the 50bp sequence, with the coordinates in the human genome
reference.
 
What is the easiest way to achieve this? Can this be done by filtering the
human sequence for certain conservation score thresholds?
 
Thanks in advance,
 
Bests,
 
A.
 
--
Albert Vilella, PhD.
Bioinformatics
 
*Cambridge Epigenetix*
Jonas Webb Building
Babraham Research Campus
Cambridge
CB22 3AT
 
01223 804261
07715 556834
 
www.cambridge-epigenetix.com
"Jones, Thomas" <thomasjones <at> fas.harvard.edu>: Mar 29 08:14PM

I'm in the process of downloading all the genomes that went into the 100-way
vertebrate genome alignment for the Eddy lab at Harvard. I'm using the
following summary page as my guide:
 
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way
 
I noticed that the "version 2, from 2014" Painted turtle link:
Painted turtle Chrysemys picta bellii Mar 2014 v3.0.3/chrPic2
 
leads to version 1, from 2011.
http://genome.ucsc.edu/cgi-bin/hgGateway?db=chrPic2
 
Even though "db=chrPic2".
 
The FTP link from that turtle page definitely goes to chrPic1 rather than Pic2.
ftp://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/
 
I tried to cheat at change the above address to Pic2, but it doesn't exist.
 
My question is this -- is the summary wrong, and the 100-way vertebrate
alignment did not use chrPic2 from 2014? Or is the link pointing to the
wrong genome version? In which case, where can I download chrPic2?
 
Thanks,
Tom Jones
Eddy Lab
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Gmane