Question: UCSC Transcriptome File
gravatar for cbio
4.2 years ago by
cbio450 wrote:

I'm looking for a UCSC Trascriptome file for hg19 and hg38 that can be used for psuedo and lightweight aligners like Salmon and Kallisto. I know that the Ensembl annotation can be found easily by looking for the cdna file, but I haven't had much luck in finding a UCSC version.

From what I read the UCSC version is a mrna.fa file available via their UCSC Browser Downloads, but I would like to double check.

Thank you!

transcriptome rna-seq ucsc • 1.6k views
ADD COMMENTlink modified 4.2 years ago by Devon Ryan97k • written 4.2 years ago by cbio450
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

It's mostly a question of whether you want to use refseq or not. If you do, then use refMrna.fa files. If you prefer a more frequently updated (and therefore less reproducible latter if you download the file again) dump from genbank then go for mrna.fa. I would suggest using refseq for something like this, it turns out that you get a little better results from Salmon (and presumably Kallisto, but we use Salmon much more frequently) if you use a transcriptome with only the most likely isoforms present.

ADD COMMENTlink written 4.2 years ago by Devon Ryan97k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1175 users visited in the last hour