Entering edit mode
2.3 years ago
MMAThijssen
▴
10
I preprocessed my data with PRINSEQ including filtering and trimming:
prinseq-lite.pl -fastq forward.fq -fastq2 reverse.fq -min_qual_mean 20 -min_len 50 -trim_qual_right 20 -trim_qual_window 15 -trim_qual_step 5 -trim_qual_type min -out_format 3 -out_good filtered.qc -out_bad null
For the sequences in filtered (out_good), I had expected them to be at least 50bp. It does not seem to be the case. There are shorter sequences present, for example of 1 bp long.
My question is: Is it true that the filter step is not the last step executed by PRINSEQ, thus is it possible to have sequences shorter than min_len? (Or did I miss something, getting these results?)