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  • extrat unaligned reads from unmapped.bam (tophat)

    Hi guys,
    I want to extract unaligned paired reads from unmapped.bam(tophat output) in fastq fomat, is there any easy way to get those reads?

  • #2
    I think there is a setting on TopHat that will output the unmapped reads to a separate file; I thought that by default, Bowtie will not output them.

    In general, unmapped reads will have the 4 flag set in the .bam, so something like

    Code:
    samtools view -f 4 sort.bam > unmapped.bam
    Will pull unmapped reads out of a .bam that has unmapped reads in it.

    Comment

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