Question: the track part of UCSC table browser
gravatar for mikysyc2016
12 months ago by
mikysyc201650 wrote:

Hi all, I prepare to download annotation file(gtf) from ucsc to do rna-seq analysis, but i can not download directly. So i preapare to download mouse txt file and use genePredToGtf to transfer it to gtf file. I have a question, the table browser page has "track:" ,it has different choice. like ucsc genes sgp genes and so on. which one should i choose? Thanks!

ucsc rna-seq gtf table browser • 412 views
ADD COMMENTlink modified 10 months ago by Denise - Open Targets5.0k • written 12 months ago by mikysyc201650

I've added the tags UCSC, GTF and Table browser to your query. People on BioStars use the tags to search for questions that they might be able to answer, and follow relevant tags with My Tags, so judicious use of tags can help people to find and answer your questions. We recommend tagging with the name of the tool you are trying to use, the type of analysis you're trying to do and the file-types you're working with.

ADD REPLYlink written 12 months ago by Emily_Ensembl18k

Why can't you download a GTF directly?

ADD REPLYlink written 12 months ago by Emily_Ensembl18k

Thank you for add the tag for me. They have the same gene id and transcript id, which will effect the analysis later (This can lead to problems with downstream analysis tools that expect exons ofdifferent isoforms to have the same gene_id, but different transcript_ids.).

ADD REPLYlink written 12 months ago by mikysyc201650

Have you tried downloading alternative GTF files, eg Ensembl?

ADD REPLYlink written 12 months ago by Emily_Ensembl18k
gravatar for Denise - Open Targets
10 months ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

Tracks are different annotations that can be added to your view in the UCSC genome browser; so it's really up to you which one to choose. They are aligned to the genome and can be either computed by UCSC or provided by others.

Do you want the ab initio prediction only? Then, choose AUGUSTUS. Are you interested in a set of annotations of the coding genome that is an agreement between several resources? Then choose CCDS. And so on so forth.

Selecting the "output format" as GTF and then hitting "get output" works for me:

Screenshot from UCSC Table Browser

ADD COMMENTlink written 10 months ago by Denise - Open Targets5.0k
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