how to make BBmerge produce same strand fastq file

Question

[shangguandong1996]

Hi, everyone

I have paired-end fastq from target amplification and want to merge them using BBMerge. But I find it seems there are two strands reads in the final merge fastq. I know it is becasue there are two strand reads in my fq1 or fq2, just like

https://github.com/shangguandong1996/picture_link/blob/main/BBMerge_fastq.jpg

so the final merge fastq have two strand reads. just like

https://github.com/shangguandong1996/picture_link/blob/main/BBmerge_merge.jpg

I am wondering whether I can only get the plus strand reads. Because the fq is the CRISPR-Cas9 screen data, and only the plus strand reads have the same squence as sgRNA. I can not simply trans-rev fq1 or fq2, because the plus and minus strand are mixed in the fq1 and fq2

Best wises

Guandong Shang

[GenoMax]

You can filter the merged reads using bbduk.sh to keep only the reads that have the sequence you want. Something like this should work:

bbmerge.sh in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq other_options | bbduk.sh in=stdin.fq outm=keep.fq.gz literal=sequence_you want