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Hi,
Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?
Thanks
Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?
Thanks
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Not that I know of, but as a workaround, you could convert to fastq and then use Trimmomatic or FastX.Originally posted by mehc View Post -
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.Originally posted by pbluescript View Post
@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?Comment
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