Hi, I'm trying to to compute the average exon expression value (mcov - multi-map-corrected average per-base read coverage) in a gene, based on output from Stringtie. As of now, I'm summarizing the mcov from each exon in each transcript in each gene, and dividing it by the total number of exons in the gene. However, I've realized that in the Stringtie output, one exon only have a single mcov value, but one exon can be part of multiple transcripts. I would expect a value based on average per-base read coverage to be dependent on the length of the transcript the exon originates from, and I'm therefore expecting different values for the same exon in different transcripts (given that not all transcripts of a gene have the exact same length).
Is my approach for computing gene average exon expression OK, or have I misunderstood Stringtie's mcov-values?
Thanks in advance!
