GENCODE track is lost
Maartje.v...@radboudumc.nl
Dear UCSC Genome Informatics Group,
We wanted to download the human GENCODE data (version 30) from the Table Browser, but then we could not find the GENCODE track anymore. Is this something you removed from the UCSC browser or was it accidentally being removed?
The files we would like to have are:
gencode.v20lift37.basic.annotation.txt
&
gencode.v30lift37.pseudogenes.txt
In case we’ve found a bug, it is possible to send us the data already?
Thank you in advance!
Maartje van de Vorst, B.ASc.
Bioinformatician
Room 5.10 (Route 848)
M.325.05.207
Radboudumc
Radboud universitair medisch centrum
Department of Human Genetics
P.O. Box 9101, 6500 HB Nijmegen (route 848)
www.radboudumc.nl/genetica
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Luis Nassar
Hello Maartje,
Thank you for your interest in the Genome Browser and for your question regarding GENCODE tracks.
A change in our system had some unintended consequences which led some tracks (such as GENCODE) to temporarily disappear from the hg19 assembly. This has since been fixed.
Regarding the gencode.v30lift37 annotations, they are currently on our development server and not yet on our live site. These data will be available on our preview server on Sunday (http://genome-preview.cse.ucsc.edu/cgi-bin/hgTables).
Do note that all data on our development server have not yet gone through our QA process and are subject to change at any time.
I hope this is helpful. If you have any further questions, please reply to gen...@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 genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
Training videos & resources: http://genome.ucsc.edu/training/index.html
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
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Maartje.v...@radboudumc.nl
Dear Lou,
Thank you very much. This was very helpful.
Do you have any idea when the gencode.v20lift37.basic.annotation.txt will go live?
Kind regards,
Maartje
From: Luis Nassar [mailto:lrna...@ucsc.edu]
Sent: donderdag 30 mei 2019 2:11
To: Vorst, Maartje van de
Cc: Wieskamp, Nienke
Subject: Re: [genome] GENCODE track is lost
If you would like to access the data before it is on our preview server, you can go to our development server with the following address (example of Table Browser for wgEncodeGencodeV30lift37): https://genome-test.gi.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=genes&hgta_track=wgEncodeGencodeV30lift37&hgta_table=0&hgta_regionType=genome
Do note that all data on our development/preview server have not yet gone through our QA process and are subject to change at any time.
Lou Nassar
UCSC Genomics Institute
Jairo Navarro Gonzalez
Hello Maartje,
Thank you for using the UCSC Genome Browser and sending your follow-up question. Unfortunately, we do not have any plans at this time to release the GENCODE v20 annotations to our live website as we are actively working on adding the most recent annotations from the scientific community to the Genome Browser.
If you have any further questions, please reply to gen...@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 genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/196b09181bc44e20ba719ffbc3f7de88%40Umcexchp06.umcn.nl.
Maartje.v...@radboudumc.nl
Dear Jairo,
I am sorry, I made a typo. The question is: Do you have any idea when the gencode.v30lift37.basic.annotation.txt will go live?
So not v20..
Kind regards,
Maartje van de Vorst
Daniel Schmelter
Hello Maartje,
Thank you for clarifying your question. We have noted your request to add the Gencode.v30lift37 data to our public site, but we cannot give specific dates when that may be available. We appreciate your request and will factor that into our data release prioritization.
In the meantime, you can access that data through the Table Browser on our Genome-Preview site (https://genome-preview.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_track=wgEncodeGencodeV30lift37). Please be aware that this data is still under review by our Quality Assurance Team. You may also be interested in the v30lift37 files directly from GENCODE (https://www.gencodegenes.org/human/release_30lift37.html).
If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genomics Institute
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/809780ab907c41fd8f0efecd9f140643%40Umcexchp06.umcn.nl.