Hi.
I might be doing something incorrect, but I find one-base and other short exons in TCGA and GTEx exon count data. I wasn't able to find an explanation in your Genome Biology paper, so I would appreciate a pointer if it's there somewhere.
> load("rse_exon_bile_duct.Rdata")
> rse_exon@rowRanges[]
GRanges object with 603139 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
ENSG00000000003.14 chrX [100627109, 100628669] -
ENSG00000000003.14 chrX [100628670, 100629986] -
ENSG00000000003.14 chrX [100630759, 100630866] -
(...)
> rse_exon@rowRanges[520:522]
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
ENSG00000001631.15 chr7 [92245913, 92245914] -
ENSG00000001631.15 chr7 [92245915, 92245915] - <<<<<<<<<<<<<<<<<<<
ENSG00000001631.15 chr7 [92245916, 92245920] -
If these short exons are artifacts, are they "stealing" counts from legitimate exons? If so, is there a rational way to recapture these counts, like adding the counts to the longest overlapping exon, or is it safe to just ignore them? Should I be using derfinder?
Thanks.