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  • jomaco
    replied
    Thanks. Very useful, I wasn't aware you could combine -F and -f

    Leave a comment:


  • swbarnes2
    replied
    Throw a -F 4 in there too, or you will get unmapped reads whose mate also did not map.

    Leave a comment:


  • jomaco
    started a topic Samtools filtering

    Samtools filtering

    Hi

    I am trying to filter for those reads which are mapped but where the mate is unmapped.

    I tried:

    Code:
    bsub "source samtools-0.1.18; samtools view -bt -f 8 F3H.fa.fai L2557F3H.sam > L2557F3H.bam"
    This doesn't appear to have worked correctly.

    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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