Samtools And Cuffdiff

Question

[disco]

OK, here we go.. I want to see differential expression for two genes at a genomic locus in different cell lines. I have a set of bam files of long RNA seq for this. Q-1: Is it possible to convert all the bam files into sam together? After this I would proceed to input sam files into cufflinks to generate gtf files. Q-2: How do I proceed from here to compare differential expression across different samples?

Answer 1

[biorepine]

It should be simple. Run your samples like this. I think cuffdiff should work on bam files as well so no need to convert bam into sam.

cuffdiff your_transcripts.gtf cellline1.bam  cellline2.bam cellinen.bam

fyi : http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff