I am new to the galaxy server, and I want to analyse my RNA-seq data with the following standard pipeline (TopHat=>Cufflinks=>Cuffmerge=>Cuffdiff) to determine differential expression between control and treatment group. However, both cufflink and cuffmerge only generate GTF file type but for Cuffdiff, they use BAM, so the only file i can use to run cuffdiff is the TopHat-generated files... But then what is the point to do Cufflinke and Cuffmerge exactly? Sorry guys, I am quite confused here.
Thanks in advance for answering my questions,