Question: Samtools And Cuffdiff
0
gravatar for disco
6.5 years ago by
disco30
disco30 wrote:

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?

cuffdiff • 1.8k views
ADD COMMENTlink modified 6.5 years ago by biorepine1.4k • written 6.5 years ago by disco30
1
gravatar for biorepine
6.5 years ago by
biorepine1.4k
Spain
biorepine1.4k wrote:

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

ADD COMMENTlink written 6.5 years ago by biorepine1.4k
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