Question: Why run FeatureCounts after Stringtie? (Galaxy recommends!)
gravatar for c_u
18 months ago by
United States
c_u290 wrote:


I have RNA-Seq data from patients, and I want to find novel transcripts that are differentially expressed in the treatment condition. For this, I followed the methodology given in this Galaxy tutorial - Here they use HISAT for mapping, followed by Stringtie for transcript reconstruction (using Stringtie allows them to find novel transcripts), and then use FeatureCounts for counting the number of reads per transcript. Then they use DESeq2 for differential expression analysis.

My question is that since Stringtie itself also gives the count (in terms of coverage, FPKM and TPM) for each transcript that it constructs, then why should I use FeatureCounts for these constructed transcripts?

rna-seq • 1.5k views
ADD COMMENTlink modified 18 months ago by kristoffer.vittingseerup3.5k • written 18 months ago by c_u290

DESeq2 requires raw counts, which featureCounts provides.

ADD REPLYlink written 18 months ago by GenoMax96k
gravatar for kristoffer.vittingseerup
18 months ago by
European Union
kristoffer.vittingseerup3.5k wrote:

There is absolutely no reason to do that. Actually you should rather use StringTie's quantification since that is more accurate than featureCounts - you can read more about such considerations here. Acutally DEXSeq directly supports analysis of StringTie data via tximport::tximport() as described here - although they actually don't mention StringTie in the DESeq2 vignette tximport does support StrigTie as describe here.

ADD COMMENTlink written 18 months ago by kristoffer.vittingseerup3.5k

Hi Kristoffer, did you mean DESeq or DEXSeq?

ADD REPLYlink written 18 months ago by c_u290
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