From cuffmerge to cuffdiff: Which .gtf files should be merged if assession differential gene expression

Question

[BioinfGuru]

I want to measure differential gene expression between controls (4 replicates) and treated (3 replicates)

I am about to merge all seven .gtf files for cuffdiff however, which of the 4 cufflinks output .gtf files should I be merging to look for differential gene expression?

1) genes.fpkm_tracking

2) isoforms.fpkm_tracking

3) skipped.gtf (obviously not this one)

4) transcripts.gtf

Thanks in advance. Kenneth

[GenoMax]

transcripts.gtf

See step 2 in Nature Protocols article for proper formatting of the cuffmerge command and the file you need where you specify the individual transcript.gtf files from 7 runs.