Question: Downloading genes annotations from UCSC Table Browser
0
gravatar for khorms
2.3 years ago by
khorms30
Moscow
khorms30 wrote:

I want to download genes annotations from UCSC Table Browser. Although, all the tables I found there (including refSeq, GENCODE, UCSC Genes and some others) included information for mRNA transcripts but not for genes. It means, that for a single gene any of these tables contains several lines describing different transcript variants. I want a table containing a single line per every gene. Where can I find it? Thank you.

ADD COMMENTlink written 2.3 years ago by khorms30

Does that make sense? What should that line contain if that gene has multiple alternative transcripts?

ADD REPLYlink written 2.3 years ago by WouterDeCoster39k

Every line should contain the coordinates of gene and its name. As far as I know, the cross-spliced transcripts (the transcripts made of exons from different genes) are not included in these annotation files, so all the transcript variants of the same gene should belong to the same genomic region. So if we take all the transcript variants of the same gene and merge their coordinates then we get the coordinates of gene. It can be made as a separate procedure but I'm sure it has been done already so I wonder where can I find this information. And of course yes, for some kind of analysis it makes sense because number of transcript variants can give additional bias.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by khorms30
1
gravatar for PoGibas
2.3 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Why to download GENCODE from UCSC, but not from https://www.gencodegenes.org directly? As far as I remember their annotations contains "gene" information too.

ADD COMMENTlink written 2.3 years ago by PoGibas4.8k

That works, thank you!

ADD REPLYlink written 2.3 years ago by khorms30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1053 users visited in the last hour