The Yeo lab uses a special gene definition file internally (details available upon request).
Some RNA-binding proteins (RBPs) bind before an RNA is processed, others after, and the likelihood that a peak is significant changes with respect to the biology of that RBP.
This method uses a window of 1 k B in each direction of a putative peak to define FDR and poisson significance and serves to pick up peaks which would be otherwise missed with genome-wide or gene-wide thresholds.
Approach this option with caution, but please do approach it. Clipper outputs a bed8 file: chromosome, genomic_start, genomic_stop, cluster_name, min_pval, strand, thick_start, thick_stop cluster_name contains the gene name, the number of reads in the cluster and a counter to give the cluster a unique identifier.
We define the bounds of a peak as the points on the fitted curve which fall below FDR or are local minima above the FDR.
This achieves a greater resolution and allows us to disambiguate multiple binding sites which are close to one another, as opposed to clumping them together.