Question: Reference for Salmon
0
gravatar for jh
22 months ago by
jh20
jh20 wrote:

Hi,

With Salmon, reads are mapped against the transcriptome and not the genome. Is it possible to use an extracted transcriptome from the human genome prepared for RSEM?

Thanks!

rna-seq • 1.8k views
ADD COMMENTlink modified 22 months ago by Rob3.3k • written 22 months ago by jh20
1
gravatar for Rob
22 months ago by
Rob3.3k
United States
Rob3.3k wrote:

Yes, if you prepare a reference with rsem-prepare-reference it will work with salmon.

ADD COMMENTlink written 22 months ago by Rob3.3k

Rob: Which transcriptome reference file do you recommend I build the index from? And where can I get such files? :) I want to analyze two different outputs: (1) isoforms of known genes in the human genome, and (1) total transcript abundance of known genes in the human genome with HGNC gene names.

ADD REPLYlink written 22 months ago by jh20

I generally like the GenCode reference, since it's fairly comprehensive and you can get the sequences directly (rather than having to build them from the genome + gtf). You can also get just the protein-coding transcripts if you want. I generally shy away from e.g. the complete Ensembl transcriptome since it includes many exact duplicate sequences (with different names), that should generally be filtered out or collapsed before quantification.

ADD REPLYlink written 22 months ago by Rob3.3k

Thank you so much!! :D

ADD REPLYlink written 22 months ago by jh20

Some papers used RSEM for transposable elements/repeats quantification. Does this mean I can use the rsem-prepare-reference of the repeat library, and feed it into Salmon?

ADD REPLYlink written 22 months ago by azlanazali010

Users have had success using salmon for such quantification tasks before. So, if you provide it with the proper reference, yes; it should work as well as RSEM for this task.

ADD REPLYlink written 22 months ago by Rob3.3k
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: 810 users visited in the last hour