Dear DEXSeq and FeatureCounts team
I was wondering if it is possible to better integrate DEXSeq with featureCounts (either the RSubread or the command line version) output, so that users don't have to modify the FeatureCounts output to convert into DEXSeq acceptable format. I have been doing this by adding Exon IDs (E1,E2..) to the gene names followed by inputting it to DEXSeqDataSet command. However still I found that some of the plots didn't work properly (probably that's not the best way to do it). It would be great to have something like DEXSeqDataSetFromFeatureCounts function, or probably getting RSubread output in a SummarizedExperiment format. However, I would appreciate any advice on this issue.