Question: Quantifying overlapping RNA-seq paired-end reads
0
gravatar for biofalconch
9 months ago by
biofalconch390
Mexico
biofalconch390 wrote:

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 • 278 views
ADD COMMENTlink modified 8 months ago by liruiradiant10 • written 9 months ago by biofalconch390
1
gravatar for Devon Ryan
9 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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

ADD COMMENTlink written 9 months ago by Devon Ryan88k
0
gravatar for liruiradiant
8 months ago by
liruiradiant10
United States
liruiradiant10 wrote:

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

ADD COMMENTlink written 8 months ago by liruiradiant10
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