Samtools And Cuffdiff
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?
1 answer
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
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