Closed divy-kangeyan closed 6 years ago
@Divyagash Trimming can result in one of a pair being completely removed. So you may not end up with pairs at the end. You need to use dropse
to remove those.
Here's one workflow you can use:
seqtk mergepe R1 R2 | seqtk trimfq - | seqtk dropse > R12.trim
seqtk seq -1 R12.trim | gzip > R1.trim.gz
seqtk seq -2 R12.trim | gzip > R2.trim.gz
If you are using Bash or Zsh you can do it all on one line:
seqtk mergepe R1 R2
| seqtk trimfq -
| seqtk dropse \
| tee >(seqtk seq -1 | gzip > R1.trim.gz)
| seqtk seq -2 | gzip > R2.trim.gz
@Divyagash can you close this issue please?
I used seqtk trimfq to trim paired end fastq files separately. After trimming when I try to align it I get an error saying
Paired read names do not match
Is there a way to trim paired end reads simultaneously?