Is possible to use NOISeq with counts from RSubread?

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Marcelo Laia ▴ 450

@marcelo-laia-2007

Last seen 3.1 years ago

Brazil

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?

noiseq rsubread tophat bowtie bowtie2 • 1.0k views

ADD COMMENT • link 5.5 years ago Marcelo Laia ▴ 450

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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?

ADD REPLY • link 5.5 years ago Wei Shi ★ 3.6k

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