Hello Biostars community,
I have PE samples mapped with STAR and i want to count the number of uniquely mapped reads using samtools. i did the following (using the Alex Dobin's advice in this link: https://groups.google.com/forum/#!topic/rna-star/pQbqeQd0lNY) :
SE: $ samtools view -c -q 255 -F 0x2 Aligned.out.bam PE: $ samtools view -c -q 255 -f 0x2 Aligned.out.bam
however the SE +PE/2 read count is more the number of uniquely mapped reads in my STAR log.final.out file.
To be more specific, my calculations with samtools add up to :
34 (SE) + 70579527 /2 (PE) = 35289797.5 reads.
The star total unique mappers is 35289751 reads (ie. 46.5 reads less than the samtools count) .
I have tried with a different sample, and still get 46.5 reads more with samtools.
Does anyone know why I'm getting this discrepancy?
Thank you for your help.