Soft clip / trim within unaligned .bam file

[mehc]

Hi,

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

Thanks

[pbluescript]

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.

[arvid]

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?