Retrieving BAM files from known isoforms

Question

[priscillamorris90]

Hi. I'm just wondering how to retrieve BAM files from the isoforms that I i generated from the RNA seq data? I have a few isoforms that I would love to study in details. I have the sequence. I just need to know how do i get the BAM format for these particular isoforms in order for me to determine if there is any mismatch occurred?

Answer 1

[Pierre Lindenbaum]

export your bam to bed12 : http://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html and look in the resulting file if your transcripts are here.

[priscillamorris90]

thank you for your advise! will try and see and will let you know.