samtools view -q 30 filter out most of my reads

Question

[yachen]

I used the samtools view to filter my alined reads using STAR. But when I set the q-30. most of my reads were filtered out. I changed to q-10, q-20 and I got the same amount reads. When I change to q- 0. I got more reads than my input, which is real weird. So what is the q stand for, or what kind of quanlity score? Is that because of my alimnent quanlity is too poor?

Answer 1

[h.mon]

It seems most of your reads are multi-mappers, which would explain both their low quality score and the fact you recover more reads than the input files. STAR gives a score of int(-10*log10(1-1/Nmap)) for multi-mappers, if I did the math correctly, for a read that map to 2 locations, its mapping score is 3.

What is the output of:

samtools view file.bam | cut -f2 | sort | uniq -c