genome | 25 May 19:29 2016

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

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: May 25 10:28AM -0700

Hello Minggui Chen,
 
Thank you for your question. You can retrieve the conservation score for
individual bases by creating a custom track of your regions, then
intersecting it with the Conservation track using the Table Browser. Please
see this previously answered question for more details and instructions:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/JcKxFpz0W5Y/xt2o_wz7Zt8J
 
For more information on Custom tracks, please see:
http://genome.ucsc.edu/goldenPath/help/customTrack.html
 
 
*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
 
 
 
 
Sofia Pinto <sofiapinto <at> coimbra-genomics.com>: May 25 01:46PM

Hi,
 
I am using the executable version of the liftOver tool.
I performed the liftOver of some SNPs from GRCh38 to GRCh37 and everything went ok with the liftover of the positions.
However, in some of the SNPs the alleles were inverted, meaning that the reference/alternative allele in 37 was the alternative/reference allele in 38.
 
As an example:
(37) rs1985842, 22, 42523409, G, T
(38) rs1985842, 22, 42127407, T, G
 
I would like to know if there is a strategy to deal with such cases?
Are there any scripts/tools that can be used to handle the inversion of the alleles after liftOver?
 
Thank you for your attention.
 
Best regards,
 
Sofia Pinto, PhD
Bioinformatics Specialist
Coimbra Genomics S.A.
 
skype: fiapinto
www.coimbra-genomics.com<http://www.coimbra-genomics.com/>
Yuval Nevo <yuval.nevo <at> mail.huji.ac.il>: May 25 09:29AM +0300

Hello UCSC Genome Browser team,
I am working with the current tables of the hg38 human assembly.
I am trying to merge information from the knownGene and kgTxInfo tables,
according to the name field. However, while the knownGene table has 195178
unique gene names, and the kgTxInfo table has 104178 unique gene names, the
overlap contains only 9459 genes.
I did notice that in several cases there are version differences (for
example, uc001aak.4 in the knownGene table appears as uc001aak.3 in the
kgTxInfo table). It seems that the kgTxInfo table is not up to date...
Is there a reason for this low overlap of gene names? can I ignore the
version and merge by the initial 8 positions of the name? Is a new kgTxInfo
table to be placed in the annotations directory soon?
Thanks a lot, Yuval.
Christopher Lee <chmalee <at> ucsc.edu>: May 24 02:36PM -0700

Hi Shelly,
 
The wgEncodeGencodeBasicV23 table does not contain any data generated by
the Mendell Lab. For more information on how the data in the this table
was generated, please see the track description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV23
 
Note that you can still download the data from the custom tracks through
the Table Browser. If you navigate from the lab's session link:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mendelllab&hgS_otherUserSessionName=Manuscript%2Dhg19
 
to the Table Browser through the Tools menu at the top of the Genome
Browser page (after loading the session), you can use the custom tracks
as if they were native Genome Browser tracks and filter, intersect and
select fields from the custom tracks.
 
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.
 
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: May 24 01:14PM -0700

Hello Mehar,
 
Thank you for your question. One of our engineer notes that you can pick up
the repbase library from:
 
http://www.girinst.org/
 
file: RepeatMaskerLib.embl
 
This file contains species indication and repeat identifier as seen from
this grep: egrep "RepbaseID:|Species:" RepeatMaskerLib.embl
 
The version we have been using in recent times is from 31 Jan 2014
'20140131'.
 
 
*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 Tue, May 17, 2016 at 4:05 PM, Arumilli, Meharji <
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genome | 16 May 19:25 2016

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

Shelly M <shelly.mh <at> gmail.com>: May 15 10:31PM +0300

Hello,
 
Is there a way to get annotation of pri-miRNA?
From the paper that was published last year in Genome Research
<http://genome.cshlp.org/content/25/9/1401.full> it is said that those
annotations should be available at UCSC browser, but I couldn't find it..
 
I would really appreciate your help,
Thanks
Shelly
Mark Brown <mbrown89 <at> gmail.com>: May 15 04:09PM -0700

ensGene table is available under hg16 to hg19 schema, but is missing in
hg38.
Thanks!
Boel Brynedal <Boel.Brynedal <at> ki.se>: May 15 07:48PM

Hi,
 
I am using the Table browser to download BED files for SNPs (snp146Common) by uploading a list of identifiers. I am submitting rather long list of identifiers (2.5 million) and this seems to be working OK, and the download concludes without any errors. But the resulting file lacks a couple of identifiers and the last row is not finished. As:
 
$ tail -n 3 /Users/Boel/Downloads/meta_snps_aa.bed
chr22 50620689 50620690 rs3091400 0 -
chr22 50622239 50622240 rs9628229 0 +
chr22 50622770 50622771 rs$
 
It is only the last < 100 identifiers that are missing and the problem remains if I ask for ~1 million identifiers. Can one not ask for a large number of identifiers, and what is the upper limit in that case? Querying for ~30 SNPs did not cause any issues.
 
I am using the european mirror in Chrome.
 
Thanks,
Bo
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genome | 11 May 19:28 2016

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

camille Simonet <camille.anna.simonet <at> gmail.com>: May 11 04:17PM +0200

Hi,
 
I want to liftOver hg38 to rheMac3. This pair of genomes is available from
the UCSC website liftOver tool pullbar menu, however, I cannot find the
chain file in the liftOver of rheMac8.
 
Is this chain of hg38torheMac8 available somewhere?
 
Thank you,
CS
Matthew Speir <mspeir <at> soe.ucsc.edu>: May 11 08:57AM -0700

Hi Camille,
 
Thank you for your question about downloading the hg38ToRheMac8 LiftOver
chain file.
 
The LiftOver chain files are always found in the "LiftOver" directory
for your original or starting assembly. In this case, since you are
converting coordinates from hg38 to rheMac8, your original/starting
assembly is hg38. You can find the LiftOver files for hg38 on our
download server under the "LiftOver files" link for hg38 here:
http://hgdownload.soe.ucsc.edu/downloads.html#human.
 
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 5/11/16 7:17 AM, camille Simonet wrote:
Lance Parsons <lparsons <at> princeton.edu>: May 11 11:15AM -0400

I have started working with a lab that does research on Ciona and we
have noticed that there are two new genomes available in the "test" UCSC
genome browser. I'm right now trying to get a handle on the current
state of reference genomes and annotations and setup some standards for
the lab. I have a couple of questions about the two ciona species on UCSC:
 
1. Is there any known timeframe when they (ci3 and cioSav2) will be
available in the main UCSC browser? Are there things we can do to help
with that?
 
2. Can you tell me specifically which references will be used for Ciona
intestinalis (ci3) and Ciona savignyi (cioSav2)? Also, which gene
annotations will be loaded for these?
 
Thanks for any information you can provide. Having a standardized set of
tools at UCSC is very helpful and we look forward to building those up
for the ciona species.
 
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University
Christopher Lee <chmalee <at> ucsc.edu>: May 10 12:20PM -0700

Hi Varun,
 
Thank you for your question about obtaining cell specific SNPs for a list
of genes.
UCSC does not have cell specific genome data readily available, as it is
embedded within
1000 Genomes data. Please see this previously answered mailing list
question for more
information:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_LYgzhxj3xo/lY83BBNLHgAJ
 
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 | 6 May 19:24 2016

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

Christopher Lee <chmalee <at> ucsc.edu>: May 05 04:06PM -0700

Hi Aishwarya,
 
Thank you for your question about how to use the reciprocal best chains
file.
 
Questions about how to process data fall outside the scope of this mailing
list,
thus how you choose to use the rbest file is up to you.
 
We recommend Biostars: https://www.biostars.org/
to get help with more general questions like this one.
 
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, May 2, 2016 at 6:38 PM, aishwarya kulkarni <sharkashu <at> gmail.com>
wrote:
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: May 05 11:58AM -0700

Hello Nefertiti,
 
Thank you for your question about obtaining a list of genes near your SNP.
 
The instructional video was produced using the hg19 assembly of the
human genome assembly, which includes a "UCSC Genes" track. Since the
video was produced, we switched our default assembly to the newer hg38
version of the human genome assembly. The hg38 assembly does not include
a UCSC Genes track, however, it includes a similar track called "GENCODE
v22".
 
If you want to continue using the hg38 assembly as you are now, then you
can just select this "GENCODE v22" from the track drop-down on the Table
Browser and the rest of the instructions in the video should remain the
same. However, if you want to follow those instructions in the video
exactly, then you will need to switch to the hg19 assembly. To do so, in
the Table Browser, ensure that you have selected "Mammal" from the
"clade" drop-down menu, "Human" from the "genome" drop-down, and "Feb.
2009 (GRCh37/hg19)" from the "assembly" drop-down.
 
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 5/4/16 10:23 AM, Nefertiti Ojinjideka Hemphill wrote:
Xiaomao Zhu <Xiaomao.Zhu <at> qiagen.com>: May 05 05:43PM

Dear UCSC genome stuff,
We have been downbloading xmGene table (org=Human, group=genes, track=xmGene, table=xmGene) from your tableBrowser in the past. However, t's not available any more.
Could you point to me which track/table I can use in order to get the same information?
Thank you.
Best,
Xiaomao Zhu
Camille Ezran <camille_ezran <at> yahoo.com>: May 05 05:20PM

Hi,I am a researcher at Stanford University studying mouse lemurs (Microcebus murinus). I would like to know more about the UCSC microcebus annotation. According to the website, the UCSC genome browser assembly was released in May 2015. However, when I browse for specific genes there are only non-microcebus refseq genes that come up. This is surprising to me since the NCBI refseq annotation was also released recently. Is there a reason the refseq genes do not appear in the search? How can I have access to the mouse lemur transcripts in order to align them with transcripts from other primates?
Thank you,Camille Ezran
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genome | 5 May 19:08 2016

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

"Dedeyne Sándor" <Sandor.Dedeyne <at> student.howest.be>: May 05 09:48AM

Dear Sir,Madam,
 
 
Recently I have been working on implementing multiWig tracks to the local GWIPS browser which is a mirror of the UCSC genome browser.
 
But after implementing these tracks with the aggregate stacked method we noticed that when we only select one subtrack we are shown a purple line on the top.
 
Also it shows No Data on the Y-axis.
 
Is this a bug or is this meant to be like this?
 
 
Thanks in advance,
 
 
Sándor
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: May 04 11:02AM -0700

Hello Julie,
 
Thanks for your email and my apologies for the delay in response. We have
created a BAC End Pairs track for our rat (rn6) assembly, however, it has
not yet been reviewed by our Quality Assurance team. We're not certain as
to when this might happen, but in the meantime you are welcome to view it
on our preview site:
http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=rn6&g=cloneEndSuper.
Please keep in mind that our preview site contains untested and
experimental data, and may undergo changes at any time.
 
 
*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
 
 
 
 
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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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