This may be a rehash of an earlier issue, but I'm trying to figure out why is it that summarizeOverlaps is giving me no reads in a set of bam files. In essence, when analyzing a set of bam files I got 0 reads after summarizeOverlaps, even if the bam files (a total of 30 of them) show an average of 25M reads each. The code in R:
mm10.txdb <- makeTxDbFromUCSC(genome="mm10", tablename="knownGene")
ebg10 = exonsBy(mm10.txdb,by="gene")
bamdir = dir(getwd(),pattern = ".bam",full.names=TRUE)
overlaps = summarizeOverlaps(features=ebg10,
rnaseq.counts = assays(overlaps)$counts
The "overlaps" object gives me no read counts at all, and if I do an earlier suggestion from an earlier post in including the inter.feature=FALSE flag I still get no reads. I'm wondering if you guys have ideas on what else may be going on and/or how to move past this. Thanks!