Regions are not detected as expressed

[adomingues]

I encountered a strange result while analysing RNA-seq data with derfinder. My goal is to find expressed regions in a number of conditions which broadly derfinder does. The issue is that it seems that the reported regions are smaller than what would be expected by visual inspection:

As you can see 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 now if this a setting which needs to be changed, 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
   )

files are bam files, read length = 75 and cutoff = 5. Session info can be found here.