Question: How can I use featurecounts after generating a bam file using BWA?
gravatar for a.rex
13 months ago by
a.rex210 wrote:

I have a reference transcriptome, to which I have aligned reads using BWA. My goal is to quantify the aligned transcripts - how can I do this? Can I use featurescounts - bearing in mind that I have aligned to a transcript fa file.

rna-seq features counts • 463 views
ADD COMMENTlink modified 13 months ago by h.mon29k • written 13 months ago by a.rex210

I read yesterday about Salmon and Kallisto, which can generate count metrics from a transcripts.fa file and the FQ reads. Maybe they have an option to use an aligned BAM?

ADD REPLYlink written 13 months ago by RamRS26k

Salmon does, see the section of the manual :)

ADD REPLYlink written 13 months ago by ATpoint31k
gravatar for h.mon
13 months ago by
h.mon29k wrote:

If you aligned to the transcriptome, you should not use featureCounts, particularly if you have a well annotated transcriptome, or assembled the transcriptome yourself. In both cases, the transcriptome should have a lot of isoforms, which would result in a lot of multi-mapped reads, which would be discarded by featureCounts. See Why you should use alignment-independent quantification for RNA-Seq for a discussion on this.

Use RSEM in this case, or as ATpoint noted above, salmon quant.

ADD COMMENTlink written 13 months ago by h.mon29k
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