about cuffdiff input and parameters

Question

[yaminivadapally]

i have 120 sample in which 60 are controls and 60 are diseased, i ran tophat, cufflinks and cuffmerge i have merged_asm.gtf file which is output of cuffmerge. i want to run cuffdiff to find differential expression how to give command for cuffdiff,which parameters should i use?????

[WouterDeCoster]

Was the manual unclear? What have you tried?

Answer 1

[Kristoffer Vitting-Seerup]

Why not use Salmon to quantify all the fastq files using the merged transcriptome to build the index. Salmon (or Kallisto) is much more more accurate and MUCH faster Cuffdiff (see this article for a comparison).

Furthermore:

• This workflow illustrates how to do EDA and DE analysis downstream of the Salmon quantifications.
• If you are interested my R package IsoformSwitchAnalyzeR can help you statistically identify, analyse and visualise isoform switches such as the example here. Btw it also supports CuffDiff data.

Cheers Kristoffer