Variable Read Length

[dlukacso]

I have read on the MISO website that it doesn't work at all with BAM files that have mixed read lengths. My problem is that I'm working on aligning large amounts of data, and it is handled through a separate server, where I can't adjust the alignment parameters. Consequently all of the BAM files I get are of mixed read lengths.

I have managed to figure out how to get a list of all of the read lengths in a BAM file, and then for each individual read length get all the reads matching that length, put them into a separate BAM file, and run miso on that reduced BAM file. The problem is, this tends to result in more than 10 separate out_put and summary folders per original BAM file, and I'm not sure how to merge these.

Alternatively, I have seen it suggested that I should just trim the BAM file that I have to a uniform read length, but when I try to look up how to do that on google, I get recommendations that I should go back and trim the fastq files to a uniform length and realign from the beginning instead. Given my current set up that isn't very viable at the moment, so does anyone know how I might go about trimming a BAM file to have uniform read lengths and make it MISO compatible?

Either solution would be fine for me, I just don't know how to do them.