linking to a transcript

[Naomi David Swidler]

i use the knowntoensembl txt file to mine transcript ids. i link to them using a url you gave me about a year ago (see https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/Hello$20again$2C$20Naomi/genome/Q7FHGTfdPLk/VPUsf2qpBwAJ): 

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=<transcript id>.

in the most recent file, one of the transcript ids is uc003tqj.3 (corresponds to ENST00000344576). when i link to this id as above, i get an error:

Sorry, couldn't locate uc003tqj.3 in genome database

in the previous version of the file, the analogous id was uc003tqj.4. the url works using this id.

can you enlighten me about the file changes and how i should proceed to make my links work? thanks so much.

naomi rosen

[Cath Tyner]

Hello Naomi,

Thank you for inquiring about the UCID versions as they pertain to the URL you are using to link to hg38 transcripts via our Gene Description and Page Index (hgGene page).

For hg38, the UCID versions will continue to change as the default GENCODE sets are updated. For the example that you provided,

http://genome.ucsc.edu/cgi-bin/hgGene?db=hg38&hgg_gene=uc003tqj.4

The ID has been updated from uc003tqj.3 to uc003tqj.4 for hg38's GENCODE v24 release.

uc003tqj.3 can be viewed in hg19:
http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=uc003tqj.3
Data last updated for hg19.knownToEnsembl: 2014-03-05

Since this "hgGene" page must link to the UCID.version (e.g., uc003tqj.4), the url that you are using is dependent on these data; when the gene set is updated, the version number will change in some cases, thus breaking your url.

You can sign up for the UCSC Genome Browser Announcements to see when updates like this take place:

Announcements forum: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce * Subscribe: Email genome-announce+subscribe@soe.ucsc.edu * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

For example: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome-announce/GENCODE/genome-announce/ArcmSKBBhrU/w5WCWeqOBQAJ

You can always download an updated set of IDs from our Table Browser tool. For example, for hg38:

Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

Set the following fields:

clade: Mammal, genome: Human, assembly: hg38, group: Genes & Gene Predictions, track: GENCODE v24, table: knownToEnsembl

Note: You can click on the "describe table schema" button to see field columns and date of last update (hg38) "Data last updated: 2016-03-28."

Next, set the "output format" to "selected fields from primary and related tables" and click the "get output" button to go to the next step.

In the first section, "Select Fields from hg38.knownToEnsembl" select the checkbox for "name" : "Primary ID" to select UCIDs.

Select "value" "associated ID, label, quantity etc." to select the associated Ensembl ID.

Enter a name for the file to download the file.

Now click the "get output" button to query the table and receive the output in a file, which will look like this:

#name value
uc001aak.4 ENST00000417324.1
uc001aal.1 ENST00000335137.3

I've uploaded this query for you to download in the directory below, there are 197,782 records (and 1 column line).

http://hgwdev.cse.ucsc.edu/~cath/temp/hg38.knownToEnsembl.UCSCids.txt

Meanwhile, I will ask engineers if there is anything we can do to provide a more stable url for hgGene, and I will let you know if possible. 

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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