How to see what percentage of reads remain after quality filter to a certain phred score

Question

[nikelle.petrillo]

Hi all,

I ran FASTQC on my raw reads to check out some quality stats. However, I would like to see how many reads will remain if i set the phred quality score to 30. Is there a way / a tool to do this?

Thanks for the help! Nikelle

[Pierre Lindenbaum]

Count before/after: How to count fastq reads

Answer 1

[Brian Bushnell]

I'd suggest using BBDuk with various trimq thresholds; it tells you exactly how many bases are trimmed and how many reads are removed as a result:

bbduk.sh in=foo.fq out=trimmed.fq qtrim=r trimq=30

Input:                          20000 reads             3011442 bases.
QTrimmed:                       16939 reads (84.70%)    1007270 bases (33.45%)
Total Removed:                  34 reads (0.17%)        1007270 bases (33.45%)
Result:                         19966 reads (99.83%)    2004172 bases (66.55%)

[GenoMax]

Omit out=filename if you just want to see what the result/stats look like.