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Hi,
I am trying to run cuffdiff on multiple samples (650 to be precise). I ran cuffmerge on the cufflinks transcript assembly files and generated a transcripts.gtf file. My command for cuffdiff looks something like the following:
cuffdiff -p 16 transcripts.gtf 1.bam 2.bam 3.bam ... 650.bam
The last time I ran this, I aborted the command after several days.
Am I on the right path? Are there any tips/tricks to know before I resubmit this to the cluster? Would it make sense to run these for individual chromosome? The question I am after is differential splicing.
Thanks
-Jaison
I am trying to run cuffdiff on multiple samples (650 to be precise). I ran cuffmerge on the cufflinks transcript assembly files and generated a transcripts.gtf file. My command for cuffdiff looks something like the following:
cuffdiff -p 16 transcripts.gtf 1.bam 2.bam 3.bam ... 650.bam
The last time I ran this, I aborted the command after several days.
Am I on the right path? Are there any tips/tricks to know before I resubmit this to the cluster? Would it make sense to run these for individual chromosome? The question I am after is differential splicing.
Thanks
-Jaison