Dear clipper team,

I am working eCLIP results from a cytoplasmic RBP that binds to spliced mRNAs.
Reading the documentation for Clipper, it says that it automatically detects whether a read is coming from pre-mRNA or mRNA to use the proper sequence size. So I ran it with the default parameters.
In my results, it seems to have troubles calling peaks in signal coming from spliced mRNA:

It looks like it is misinterpreting the sharp increase in coverage in the exon-intron junctions as a peak, while the real coverage does not change that much between exons.

Do you have any advice for using Clipper with for spliced mRNA binding protein?

Thanks a lot.