I am trying to figure out if CuffDiff handles replicates in its timecourse option.
so it would be something like this...
cuffdiff -T sampleA_20min_a.bam,sampleA_20min_b.bam,sampleA_20min_c.bam sampleA_40min_a.bam,sampleA_40min_b.bam,sampleA_40min_c.bam sampleA_1hr_a.bam,sampleA_1hr_b.bam,sampleA_1hr_c.bam
and, of course, I would include the other options. But basically, can I use a space to separate time points and commas to separate replicates?
Thanks in advance.
so it would be something like this...
cuffdiff -T sampleA_20min_a.bam,sampleA_20min_b.bam,sampleA_20min_c.bam sampleA_40min_a.bam,sampleA_40min_b.bam,sampleA_40min_c.bam sampleA_1hr_a.bam,sampleA_1hr_b.bam,sampleA_1hr_c.bam
and, of course, I would include the other options. But basically, can I use a space to separate time points and commas to separate replicates?
Thanks in advance.
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