I have run tophat over the RNA-seq data and I got the output files : accepted_hits.bam, insertions.bed, junctions.bed, deletions.bed, unmapped.bam.
Now to find the DE genes I want to run cuffdiff over the results. Is it enough if I use the
accepted_hits.bam files + gtf file as the inputs for cuffdiff or I need to also use any other output files from tophat as well?
For example do I need to have
junctions.bed for each samples?
Thank you in advance