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Throw a -F 4 in there too, or you will get unmapped reads whose mate also did not map.Leave a comment:
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Samtools filtering
Hi
I am trying to filter for those reads which are mapped but where the mate is unmapped.
I tried:
This doesn't appear to have worked correctly.Code:bsub "source samtools-0.1.18; samtools view -bt -f 8 F3H.fa.fai L2557F3H.sam > L2557F3H.bam"
I understand the bitwise flag codes to an extent but to be honest I've just been using the "plain english" picard tool (http://picard.sourceforge.net/explain-flags.html). I don't think I understand how to specify for these codes using the minus "-f" parameter.
Thanks
Jon
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