Cufflinks skips transcript models in regions with abundant reads

[mcbiodude]

Hello, I am having a problem whereby Cufflinks sometimes doesn't generate models in regions with abundant reads (while performing de novo gene model prediction), but does in other scenarios in which reads are even less abundant.

I am using cufflinks v2.0.2 and running the following command:

cufflinks -j 0.3 --library-type ff-firststrand -o TestRegion testregion.bam

As you can see from the attached image, cufflinks generates a model for several lowly abundant regions (blue and red regions in the "TestRegion" track), but completely skips a region with high read coverage on the + strand (the orange region in the "TestFwd+" track).

Does anybody have an idea of why regions can be skipped like this?

Any help would be greatly helpful, thanks!

[emreis]

Hi,
I experiencing a similar problem, i.e. cufflinks do not output transfrags for abundant reads.
In my case it happens when a reference file is provided. The command line is:

cufflinks2.1.1 -o M1toM6.assembly.out -p 14 -g genes.gtf --library-type=fr-secondstrand -b genome.fa M1toM6.sort.bam

Does any one has a similar problem? Hints for a solution?
Thanks!