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  • Soft clip / trim within unaligned .bam file

    Hi,

    Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?

    Thanks

  • #2
    Originally posted by mehc View Post
    Hi,

    Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?

    Thanks
    Not that I know of, but as a workaround, you could convert to fastq and then use Trimmomatic or FastX.

    Comment


    • #3
      Originally posted by pbluescript View Post
      Not that I know of, but as a workaround, you could convert to fastq and then use Trimmomatic or FastX.
      These won't do soft clipping, however; you'd have to parse their output and do some wild guesswork on the clippings. I would rather take the source and make a fork instead which outputs soft-clipped SAM/BAM.

      @mehc: Do you have an aligner or assembler which accepts soft-clipped bases in a BAM as input? I haven't had that yet (for Illumina data). I've seen aligners soft-clipping bases in the output alignments, however. Or are you writing something on your own and would like to use such information?
      Last edited by arvid; 05-29-2012, 06:32 AM. Reason: more precise

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