I am using the following pipeline to analyze my RNA-Seq data to detect differences in gene expression:
FASTQ Groomer -> TopHat -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund
Do I miss anything in the pipeline or this is the correct workflow for gene expression analysis?
Also,this might be a trivial question, but when using cuffmerge it supposed to merge the two files (assembled transcripts) produced by cufflinks. However, when I try to click on two files, only one of them is marked as blue. When I try to add "Insert Addition GTF Input", nothing comes up on the list. In other words, how do I pick the two assembled transcripts files to be merged by cuffmerge?