Entering edit mode
6.2 years ago
nschurch
•
0
I'm wondering if anyone knows a convenient way of converting the precise read alignments from region of a bam file into a MSA format like multifasta, aln, msf etc
From my googling it looks like there isn't a good way of doing this but maybe my google-fu is weak today....
what's your final goal ? what would you want to do with a MSA ?
Many things potentially, including map the consequences of observed alignment information, (indels, sequence ends, splices, etc) to protein structure and whatnot. Ideally I'd like a tool that also reported the actual sequence of any bits of the aligned read sequence that are skipped at the start or end of the read rather than just replace them with '-'s; but I may be asking a lot there.
Seems likel SAM4WebLogo does the basic version so thats something at least...