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Quantifying overlapping RNA-seq paired-end reads

Hi all,

I'm working with some sequencing data, and I have noticed that all of my reads overlap with their mate, so I get a concordant alignment, however they are represented as two lines in the sam alignment. But my question is: is it ok if I use the bam file with the two lines of the alignment to produce a count matrix? I was planning to use featureCounts.

Thanks in advance for your comments!

rna-seq
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updated by liruiradiant • liruiradiant • written by biofalconch biofalconch

2 answers

Yes, that is completely normal and happens all of the time. featureCounts will handle this fine.

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written by Devon Ryan Devon Ryan

Yes, you can use the -p option to get Fragment counts, if you don't do so, you get read counts, which is twice the amount

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written by liruiradiant • liruiradiant

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