Function reference

End to End pipelining

Functions to go from alignment to peaks

bowtie_to_peak	Convert aligned file to peaks for 5r, 5f, 3r, and 3f.
bowtie_to_peak_remove_shadows	Convert bowtie aligned file to peaks after shadow removal.

Peak Calling

Functions to call peaks from Rend-seq data.

hmm_peaks	Fit peaks to the provided z_scores data set using the vertibi algorithm.
thresh_peaks	Find peaks by calling z-scores above a threshold as a peak.