Calls peaks in CLIP-seq data and estimates significance. This program was used to call peaks in Puf2p CLIP-seq datasets.
Works on .bam files as input.
Requires one library file - a .gtf of the genome.
Will do a local Poisson on the CLIP data for the assigned gene. That is, the signal across the assigned gene is modeled by Poisson.
If given a negative control, will model the negative control as a negative binomial. This is also modelled for the signal across the assigned gene.
For yeast ribosomal loci, it shifts to a local mode (1 kbp around peak).
Example:
$ python call_peaks.py -c clip.bam -t genome.gtf