I have been trying to leverage
definder's ability to detect expression without the need of an annotation to identify broad regions of expressions that we observe in certain conditions:
(not shown but there is no annotated gene in this region)
The issue is that it seems that the expressed regions reported by
derfinder are smaller than what would be expected by visual inspection. As you can see above there is quite a large expressed region of which only a fraction is detected. This doesn't seem to be an issue of low coverage because, to the left, there is a an area with similar high coverage which is not reported as expressed. This an example but I found several of these in my data.
The question is if this a setting which needs to be changed/tweaked, or is this something to be expected?
The analysis was run with the following settings:
fullCov <- fullCoverage( files = files, chrs = chrom, cutoff = 0, L = read_length, verbose = TRUE, totalMapped = total_mapped, filter = "one", mc.cores = nproc ) regionMat <- regionMatrix( fullCov, cutoff = min_cov, L = read_length, maxClusterGap = 3000L, returnBP = TRUE, verbose = TRUE, filter = "one", targetSize = targetSize, mc.cores = nproc )
Coverage was taken directly from bam files, read length = 75 and cutoff = 5. Session info can be found here.