Closed biocyberman closed 7 years ago
Hi, sorry for very brief reply, not working now. picardtools is wrong IMO, but to fix it, use cutadapt with -m 1
to filter empty reads.
I overlooked the -m
option. And I agree with you that picard is overreacting in this case :)
Thank you.
This is my original sequences:
When I ran cutadapt version 1.12 like this:
cutadapt -b CCATCTCATCCCTGCGTGTCTCCGACTCAG -b CCTCTCTATGGGCAGTCGGTGAT -o out.fastq --trim-n -f fastq in.fastq
The entry
@LD5V2:07687:11043
got written out to out.fastq with empty content:This picardtools does not allow.