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  • Samtools: Mapped reads and unmapped reads

    Hello,
    I have a problem and I don't understand the flag number to extract alignment.

    So my question is I want to extract from a bowtie alignment all the reads if one mapped and the other does'nt map to do a CV analysing after.

    I want only unmmaped reads if one pair mapped properly only.

    I tried -f 3 -F 260
    and -f 4 -F 264 but it does not give me what i want, if anyone can help me.




    ------- ----------
    Map Unmapped

    or

    ------- ----------
    Unmapped Map

    Thank you very much

  • #2
    this link may help you:

    http://picard.sourceforge.net/explain-flags.html

    maybe you are interested in -f 8

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