genome | 25 Jun 19:07 2016

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

Matthew Speir <mspeir <at> soe.ucsc.edu>: Jun 24 01:12PM -0700

Hi Juan,
 
Thank you again for reporting this error. We have now fixed the issue on
our public site and you should be able to use the Table Browser with
your assembly hubs.
 
Please let us know if you continue having any issues.
 
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 6/22/16 9:22 AM, Matthew Speir wrote:
Cath Tyner <cath <at> ucsc.edu>: Jun 24 10:33AM -0700

Hello Dmitri,
 
Thank you for using the UCSC Genome Browser and for sharing the issue
you're experiencing with the dm3 phastcons track. Apologetically, this is
currently a known issue; we are working to resolve it as quickly as
possible. At this time, I cannot share an estimated time of resolution, but
I believe it will be fairly soon. I will alert you when the work is
completed. I understand you need this for a publication, so please feel
free to check in with us about timing as needed.
 
Please respond to this list if you have further questions!
 
Thank you again for your inquiry and for using the UCSC Genome Browser.
​Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:
 
* * Post to the Public Help Forum: E*
*mail genome <at> soe.ucsc.edu <genome <at> soe.ucsc.edu>​ or search the Public
Archives <https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome>*
*​ * Post to the Mirror Help Forum: Email **genome-mirror <at> soe.ucsc.edu
<genome-mirror <at> soe.ucsc.edu> *
*or search the Mirror Archives​
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror>*
*​ * Confidential/private data help: Email **genome-www <at> soe.ucsc.edu
<genome-www <at> soe.ucsc.edu>*
 
UCSC Genome Browser Announcements List
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce> (email
alerts for new data & software):
 
* * Subscribe: Email genome-announce+subscribe <at> soe.ucsc.edu
<http://genome-announce+subscribe <at> soe.ucsc.edu/> * Unsubscribe:
Email genome-announce+unsubscribe <at> soe.ucsc.edu
<http://genome-announce+unsubscribe <at> soe.ucsc.edu/>*
 
​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
UCSC Genome Browser <http://genome.ucsc.edu/contacts.html>
 
 
On Thu, Jun 23, 2016 at 6:13 AM, Dmitri Pervouchine <pervouchine <at> gmail.com>
wrote:
 
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genome | 24 Jun 19:05 2016

Digest for genome <at> soe.ucsc.edu - 7 updates in 5 topics

"Sharma, Himanshu" <Himanshu.Sharma <at> nationwidechildrens.org>: Jun 24 04:43PM

Hi,
I am finding below error in getting KnownGenes information as mentioned in http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format
 
./genePredToGtf rheMac8 knownGene knownGene.gtf
Can't start query:
select * from knownGene
 
mySQL error 1146: Table 'rheMac8.knownGene' doesn't exist (profile=<noProfile>, host=genome-mysql.cse.ucsc.edu, db=rheMac8)
 
Could you please guide me the path of known_gene.txt dump ? Just like it is mentioned for hg19: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
 
Also could you please guide me path for related chromosome fasta files of macaca mulata (rheMac8 Assembly) .
 
We really appreciate your help in the resolution.
 
Regards,
Himanshu
Cath Tyner <cath <at> ucsc.edu>: Jun 23 04:46PM -0700

Hi Chris,
 
Thanks for using the UCSC Genome Browser and for describing the issue you
experienced with the refGene table in the Table Browser. We believe that
there was a momentary issue causing this which is now resolved. Can you
please try your query again? Please respond to this forum if you continue
to experience this problem so that we can assist you!
 
Thank you again for your inquiry and for using the UCSC Genome Browser.
​Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:
 
* * Post to the Public Help Forum: E*
*mail genome <at> soe.ucsc.edu <genome <at> soe.ucsc.edu>​ or search the Public
Archives <https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome>*
*​ * Post to the Mirror Help Forum: Email **genome-mirror <at> soe.ucsc.edu
<genome-mirror <at> soe.ucsc.edu> *
*or search the Mirror Archives​
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror>*
*​ * Confidential/private data help: Email **genome-www <at> soe.ucsc.edu
<genome-www <at> soe.ucsc.edu>*
 
UCSC Genome Browser Announcements List
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce> (email
alerts for new data & software):
 
* * Subscribe: Email genome-announce+subscribe <at> soe.ucsc.edu
<http://genome-announce+subscribe <at> soe.ucsc.edu/> * Unsubscribe:
Email genome-announce+unsubscribe <at> soe.ucsc.edu
<http://genome-announce+unsubscribe <at> soe.ucsc.edu/>*
 
​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
UCSC Genome Browser <http://genome.ucsc.edu/contacts.html>
 
 
Chris Penkett <cjp64 <at> cam.ac.uk>: Jun 24 11:05AM +0100

Hi Cath,
 
Yes it seems to work now!
 
Thanks,
Chris
 
On 24/06/16 00:46, Cath Tyner wrote:
Cath Tyner <cath <at> ucsc.edu>: Jun 23 05:13PM -0700

Hi Sarah,
 
Thanks for using the UCSC Genome Browser and for submitting your questions
regarding the Table Browser.
 
Regarding your first question, we believe that there was a momentary issue
causing this which is now resolved. Can you please try your gene name
identifiers list and bed file query again? Please respond to this forum if
you continue to experience this problem so that we can assist you further.
 
For your second question regarding the possibility of obtaining the LRG_ID
and bed file for a particular gene list (containing all gene names) of 641
genes using the Table Browser:
 
Our
​"​
LRG Regions
​"​
track (in Mapping & Sequencing) is bigBed12+ (see output of bigBedInfo -as
/gbdb/hg19/bbi/lrg.bb); its hgncSymbol column contains gene symbolic names.
​Once you select this track in the Table Browser, you can click the
"describe table schema" button to see column details.
 
​See also:​
​bigBed Track Format​ <https://genome.ucsc.edu/goldenPath/help/bigBed.html>
 
In the Table Browser, you
can create a filter and paste in all 641
​of your ​
gene names. However, many genes won't have associated LRG regions
​,​
because in our outdated track
​,​
there are
​ actually​
only 506 items.
​ We do plan to update this table, but at this time, we cannot provide an
estimated time of completion.​
 
Please respond to this list if you have further questions!
 
Thank you again for your inquiry and for using the UCSC Genome Browser.
​Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:
 
* * Post to the Public Help Forum: E*
*mail genome <at> soe.ucsc.edu <genome <at> soe.ucsc.edu>​ or search the Public
Archives <https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome>*
*​ * Post to the Mirror Help Forum: Email **genome-mirror <at> soe.ucsc.edu
<genome-mirror <at> soe.ucsc.edu> *
*or search the Mirror Archives​
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror>*
*​ * Confidential/private data help: Email **genome-www <at> soe.ucsc.edu
<genome-www <at> soe.ucsc.edu>*
 
UCSC Genome Browser Announcements List
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce> (email
alerts for new data & software):
 
* * Subscribe: Email genome-announce+subscribe <at> soe.ucsc.edu
<http://genome-announce+subscribe <at> soe.ucsc.edu/> * Unsubscribe:
Email genome-announce+unsubscribe <at> soe.ucsc.edu
<http://genome-announce+unsubscribe <at> soe.ucsc.edu/>*
 
​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
UCSC Genome Browser <http://genome.ucsc.edu/contacts.html>
 
 
On Thu, Jun 23, 2016 at 8:27 AM, Sarah Vergult <Sarah.Vergult <at> ugent.be>
wrote:
 
Sujata Bhatt <bhatts <at> ohsu.edu>: Jun 23 05:11PM

Hello,
I am having an issue while using Genome Browser/TableBrowser
 
I am using it to create a BED file
Track: RefSeq Genes
Output format: BES- browser extensible data
Send Output to : Galaxy
Table: refGene
 
When I have these settings, and I paste gene name in the paste list.
It gives me the below erroe, even though the gene is in NCBI recognizable format.
 
Warning/Error(s):
 
* Note: 1 of the 1 given identifiers have no match in table refGene, field name. Try the "describe table schema" button for more information about the table and field.
1 missing identifier(s):
abca4
 
Complete list of missing identifiers<https://genome.ucsc.edu/trash/hgt/missingIds/500291133_UZZAwU9WNKyHQygR8n47zgp7XrWr_genome_1b74_c17280.tmp>
OK
Can you please look into the issue.
 
 
I tried using Ensemble Gene too in the track box.
But it returns the same error.
 
Thanks,
Sujata Bhatt
Casey Eye Molecular Diagnostics
Portland OR
Cath Tyner <cath <at> ucsc.edu>: Jun 23 05:15PM -0700

Hello Sujata,
 
Thanks for using the UCSC Genome Browser and for submitting your questions
regarding the Table Browser.
 
We believe that there was a momentary issue causing this which is now
resolved. Can you please try your query again? Please respond to this forum
if you continue to experience this problem so that we can assist you
further.
 
Thank you again for your inquiry and for using the UCSC Genome Browser.
​Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:
 
* * Post to the Public Help Forum: E*
*mail genome <at> soe.ucsc.edu <genome <at> soe.ucsc.edu>​ or search the Public
Archives <https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome>*
*​ * Post to the Mirror Help Forum: Email **genome-mirror <at> soe.ucsc.edu
<genome-mirror <at> soe.ucsc.edu> *
*or search the Mirror Archives​
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror>*
*​ * Confidential/private data help: Email **genome-www <at> soe.ucsc.edu
<genome-www <at> soe.ucsc.edu>*
 
UCSC Genome Browser Announcements List
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce> (email
alerts for new data & software):
 
* * Subscribe: Email genome-announce+subscribe <at> soe.ucsc.edu
<http://genome-announce+subscribe <at> soe.ucsc.edu/> * Unsubscribe:
Email genome-announce+unsubscribe <at> soe.ucsc.edu
<http://genome-announce+unsubscribe <at> soe.ucsc.edu/>*
 
​Enjoy,​
 
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
UCSC Genome Browser <http://genome.ucsc.edu/contacts.html>
 
 
Cath Tyner <cath <at> ucsc.edu>: Jun 23 04:18PM -0700

Hello Kiran,
 
Thank you for using the UCSC Genome Browser and for inquiring about the
location of GRCm38/mm10 annotation files.
 
Some tables which previously existed per assembly have now moved to the
"hgFixed" database. I believe that the files you are searching for can be
found here:
http://hgdownload.cse.ucsc.edu/goldenPath/hgFixed/database/
 
Please respond to this forum if you still require assisting finding
additional files!
 
Thank you again for your inquiry and for using the UCSC Genome Browser.
​Please send new and follow-up questions to one of our UCSC Genome Browser
mailing lists below:
 
* * Post to the Public Help Forum: E*
*mail genome <at> soe.ucsc.edu <genome <at> soe.ucsc.edu>​ or search the Public
Archives <https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome>*
*​ * Post to the Mirror Help Forum: Email **genome-mirror <at> soe.ucsc.edu
<genome-mirror <at> soe.ucsc.edu> *
*or search the Mirror Archives​
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror>*
*​ * Confidential/private data help: Email **genome-www <at> soe.ucsc.edu
<genome-www <at> soe.ucsc.edu>*
 
UCSC Genome Browser Announcements List
<https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce> (email
alerts for new data & software):
 
* * Subscribe: Email genome-announce+subscribe <at> soe.ucsc.edu
<http://genome-announce+subscribe <at> soe.ucsc.edu/> * Unsubscribe:
Email genome-announce+unsubscribe <at> soe.ucsc.edu
<http://genome-announce+unsubscribe <at> soe.ucsc.edu/>*
 
​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute <https://genomics.soe.ucsc.edu/>
UCSC Genome Browser <http://genome.ucsc.edu/contacts.html>
 
 
On Thu, Jun 23, 2016 at 4:45 AM, Kiran Satone <kiran_satone <at> persistent.com>
wrote:
 
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genome | 13 Jun 19:14 2016

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

Andrew Bush <abush41 <at> gmail.com>: Jun 12 01:21PM -0400

Dear UCSCC genome expert,
 
Can we please set up a discussion on how to use some of your tools? I
would be really grateful.
 
Best regards,
Andrew Bush Ph.D.
Princeton, NJ
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genome | 8 Jun 19:21 2016

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

"宝运牙" <17714202053 <at> qq.com>: Jun 08 09:06PM +0800

Dear UCSC Genome Browser Group,
 
 
I have downloaded the GTF files from the Table browser with the options of 'Genes and and Gene Predictions->Refseq Genes->refGene->outputformat:GTF' . When I summarized the downloaded GTF file, I found that there are regions labeled as CDS which are less than 3bp length. What are these regions for? (I have read the GFF introduction, the GTF file also has the 1-based start position, right?)
 
 
As I need the GTF file for annotating the gene structure, am I correct with the options above? Or where can I download such a GTF file for hg19 assembly? Looking forward to your reply.
 
 
Many thanks and all my best.
 
 
Xue Lin
Angela Zou <angezou <at> gmail.com>: Jun 07 04:04PM -0400

Hello,
 
The new chicken genome build was made available by NCBI as of January (
http://www.ncbi.nlm.nih.gov/genome/?term=txid9031[orgn]). I wanted to
annotate some of my SNPs using Annovar and I know they download gene
annotations from ucsc. So I was wondering when the gene annotations from
the new build would be made available for download? Also, I noticed that
there are some new files updated in 2016 in the galGal4 directory (
http://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/). I was
wondering why those files were updated and whether I need to re-download
files and redo annotations. Thanks!
 
 
Sincerely,
 
Angela Zou
Vaneet Lotay <vaneet.lotay <at> ucalgary.ca>: Jun 07 05:17PM

Hello,
 
 
I have set up my own trackhub that can be hosted on the main UCSC genome browser website for the Xenopus Tropicalis and Laevis genomes. I was wondering how I can add the evolutionary conservation tracks on my track hub? Basically so we can see what genes in Xenopus are conserved in other model organism species such as human, mouse, zebrafish...etc. Could be wrong but I believe these types of tracks are shown in the comparative genomics section of the Human genome tracks, up on the UCSC website.
 
 
Can I add these types of tracks to my own trackhub, is it something downloadable from UCSC? Or do these tracks need to be produced from some third-party application while comparing every other genome to my main genome (Xenopus) in order to produce the necessary data source files for these tracks? If you can help me with this I really appreciate it.
 
 
Thanks,
 
 
Vaneet
 
 
Vaneet Lotay
 
Xenbase Bioinformatician
 
403-220-6652
 
724 ICT Building - University of Calgary
 
2500 University Drive NW
 
Calgary AB T2N 1N4
 
CANADA
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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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Gmane