Hi Thomas,
Can you be more specific?
From the Cuffdiff manual I understand that technical replicates are supported, but not biological replicates. For example, if I have 3 control and 4 disease RNA-Seq samples (all samples different), can I use Cuffdiff to analyze the differential expression between the control and the disease groups? If the answer is yes, how would I do it?
Can you be more specific?
From the Cuffdiff manual I understand that technical replicates are supported, but not biological replicates. For example, if I have 3 control and 4 disease RNA-Seq samples (all samples different), can I use Cuffdiff to analyze the differential expression between the control and the disease groups? If the answer is yes, how would I do it?
Cuffdiff manual:
Cufflinks includes a program, "Cuffdiff", that you can use to find significant changes in transcript expression, splicing, and promoter use. From the command line, run cuffdiff as follows:
cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam[,...,sample1_replicateM]> <sample2_replicate1.sam[,...,sample2_replicateM.sam]>... [sampleN.sam_replicate1.sam[,...,sample2_replicateM.sam]]
Cufflinks includes a program, "Cuffdiff", that you can use to find significant changes in transcript expression, splicing, and promoter use. From the command line, run cuffdiff as follows:
cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam[,...,sample1_replicateM]> <sample2_replicate1.sam[,...,sample2_replicateM.sam]>... [sampleN.sam_replicate1.sam[,...,sample2_replicateM.sam]]
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