A comparison of different CLIP peak calling tools. RNA maps are used to
demonstrate the differences in peak calling tools for the same iCLIP PTBP1 data
set (16). To show that the RNA maps can
be reproduced by exons defined using a different data source, we defined the
regulated exons using RNA-seq data following PTBP1 CRISPR knockout in K562 cells
from the ENCODE website. We identified the skipped exons detected using rMATS
(101) using only junction counts and
a p-value threshold of 0.05 and FDR threshold of 0.1. Silenced
and enhanced exons were defined using an inclusion level difference threshold of
0.05; control exons were selected as those with a p-value
greater than 0.1, an FDR value greater than 0.1, an inclusion level of less than
0.9, and an inclusion level difference less than 0.05. We compared the peaks
called using iCount (15) (using a
15-nucleotide peak calling half-window and 30-nucleotide clustering window),
Piranha (42) (using a 30-nucleotide bin
size and 30-nucleotide merging window), and CLIPper (25, 44) (using
default settings). For this data set, Piranha and iCount have runtimes of
∼2 minutes and ∼7 hours, respectively, using 1 processor; CLIPper
has a runtime of ∼7 days using 20 processors. The code to reproduce this
figure is available for download at https://github.com/jernejule/clip-data-science. Abbreviations:
CLIP, UV crosslinking and immunoprecipitation; FDR, false discovery rate; iCLIP,
individual-nucleotide resolution CLIP.