As far as I know, Cuffmerge when we need to perform cuffdiff. In my study I want to classify the samples based on expression level obtained from cufflinks. I am wondering if Cuffmerge step is still needed if we are only interested in expression level ? (no differential expression analysis would be performed).
asked 25 Oct '12, 16:14
You might get problems when not running cuffmerge with transcripts that only are found in a couple of the samples. Also with novel transcripts that might not have the start/stop positions in all samples. They might overlap to 99%, but if you are just 1 bp off in either position, a simple script might miss that they are the same transcript.
Cuffmerge will fix these things for you. It will write a file containing the union of all transcripts in all samples, and it will do its best to figure out which transcripts are the same or different splice forms. It can also add annotations from a GTF file if you give it one, to annotate all transcripts it can.
If you only are interested of previously annotated genes, i guess you could take the RPKM from each sample and skip running cuffmerge.
answered 25 Oct '12, 17:07