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!
Count before/after: How to count fastq reads
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%)
Omit out=filename if you just want to see what the result/stats look like.
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