Entering edit mode
I read in the NOISeq Users Guide that it use counts from TopHat. I have some trouble to use TopHat with my raw data: it is paired data. So, I ask if is possible to run RSubread, got a lot of files (I use gappedIndex=TRUE) and I think that NOISeq use only one index. Please, is it possible to you provide me a step-by-step on how I could make an Index and use it on NOISeq?
TopHat is a read aligner and it does not produce read counts. If you want to get read counts for genes you can use
featureCounts
function in Rsubread. The index you mentioned in Rsubread is used byalign
andsubjunc
for read mapping and I don't think NOISeq uses this index. So what is the 'counts' you'd like to have?