Hello, I`m trying to create an exon count object, there seems to be 2 ways Using newExonCountSet, arguments needed include counts matrix, geneID, exonID,transcriptID etc. Using read.HTSeqCounts, arguments needed include filelist, annotation file etc. How can I use read.HTSeqCounts with the argument counts as input instead of providing a file list? I already have a matrix of counts for each exon bin (created by a combination of dexseq_count.py and some processing on my end) and a flattened annotation file (obtained from dexseq_prepare_annotation.py). I understand that I could use newExonCountSet instead, but extracting the transcripts argument from the annotations file seems non-trivial, and I want to detect differentially expressed transcripts an also plot them. Please advise. Thanks, Al [[alternative HTML version deleted]]