I have paired end reads and I am performing de novo RNA seq. I used tophat to align my reads to a reference transcript I assembled in Trinity. Now, I would like to perform differential expression analyses in EdgeR. My understanding is that I can not simply input the accepted_hits.bam output file from tophat and that I need to use a program to give me a matrix of raw counts? I have decided to use FeautreCounts from the Rsubread package to produce these raw counts. However, I am new to R and this learning curve is a bit steep. Does anyone know how I should go about using FeatureCounts? I have read over the manual, there seems to be many arguments that can be used, which are necessary for RNA seq data?
Any help would be appreciated! Thanks, Nikelle