Hi,
I am using BBmap to map paired-end DNA reads to a reference and want to map pairs only without mapping individual mates similar to --no-mixed option in bowtie2.
Could someone help me with this?
Thanks!
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written
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b.shrestha •
Try the following option with bbmap.sh. I don't know if this is only referring to reads that are not a proper pair.
pairedonly=t (po) Treat unpaired reads as unmapped. Thus they will
be sent to 'outu' but not 'outm'.
Otherwise you can do something like:
bbmap.sh <options> out=stdout.bam | reformat.sh in=stdin.bam out=final.bam pairedonly=t
pairedonly=f Toss reads that are not mapped as proper pairs.
I want to toss the reads that map but don't have a pair. Thank you for your help.
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so you want BBmap to only report a mapping if both reads of a pair maps?
if so, have a look at the
pairedonly=foption (put it totfor your case)Yes, i will try that. Thanks for the help.