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Trivial question? - when aligning raw reads from a large file to a small reference sequence and 99.99..% of reads are non matches, with Flag 4, is there a flag to set to report only matches. Thanks, John
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Have a look at:
https://www.biostars.org/p/56246/ -
Thanks for the suggestion. Unfortunately it does not solve the problem of producing a 40Gb .sam file when only 1Mb of it is useful. It seems to make my computer heavier.Comment
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Have you tried piping bwa mem output into samtools? Something like:
Code:bwa mem [your options] | samtools view -SF 4 - > output.sam
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Also, BBMap has an "outm" flag, which will retain only mapped reads, but keep pairs together (if either one was mapped). For example:
bbmap.sh ref=reference.fa in1=r1.fq in2=r2.fq outm=mapped.samComment
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Many thanks for both the samtools and BBMap suggestions. I had not heard of BBMap, but was extremely impressed at its speed and the way outm worked.Comment
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