Question: Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
1
gravatar for tianshenbio
9 months ago by
tianshenbio80
tianshenbio80 wrote:

I hope to do DE analysis at both gene and transcript level.

First I mapped the reads to the genome using hisat2. Now I need to generate a raw count matrix for deseq2.

Since I have a well-annotated gff file, I am not interested in finding new isoforms. If I chose Stringtie, it would only be used to generate raw count matrix. And it can calculate both gene and transcript in one run (right?). If I chose Featurecounts, I have to run it twice, for gene and transcripts separately. But someone told me Featurecounts is not suitable to quantify isoforms...

What would be a better choice?

ADD COMMENTlink written 9 months ago by tianshenbio80

for instance salmon is well suited for isoform quantification (better than FeatureCounts of HTseq-count indeed)

with 'gene' you mean gene-locus and "transcript' = isoform(s), correct?

ADD REPLYlink modified 9 months ago • written 9 months ago by lieven.sterck10k

Yes, with 'gene' I will count reads mapped to all exons of that gene locus, with 'transcripts' I hope to quantify isoforms. Is Stringtie suitable for isoform quantification as well?

ADD REPLYlink written 9 months ago by tianshenbio80

not sure if I (can) agree with your approach here :/

sorry, don't have much hands-on experience with StringTie, but I know it can (and is used) for creating de-novo transcripts (and isoforms) from mapped reads. Others will chip in here I assume.

ADD REPLYlink written 9 months ago by lieven.sterck10k
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: 2175 users visited in the last hour
_