Question: Is possible to use NOISeq with counts from RSubread?
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12 days ago by
Marcelo Laia430
Brazil
Marcelo Laia430 wrote:

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?

written 12 days ago by Marcelo Laia430

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 by align and subjunc for read mapping and I don't think NOISeq uses this index. So what is the 'counts' you'd like to have?