Question: UCSC Transcriptome File
2
gravatar for cbio
3.3 years ago by
cbio430
cbio430 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 • 1.3k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan93k • written 3.3 years ago by cbio430
1
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k 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 3.3 years ago by Devon Ryan93k
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