Table 1. Main features of the peak detection programs used in this analysis.

	CIMS	PIPE-CLIP	Piranha	Pyicoclip
Technology	HITS-CLIP	HITS-CLIP, PAR-CLIP, iCLIP	HITS-CLIP, PAR-CLIP, iCLIP, RIP-seq	HITS-CLIP, PAR-CLIP, iCLIP, RIP-seq, CHIP-seq
Website	http://zhanglab.c2b2.columbia.edu/index.php/CIMS_Documentation	https://github.com/QBRC/PIPE-CLIP	http://smithlabresearch.org/software/piranha/	https://bitbucket.org /regulatorygenomicsupf /pyicoteo
Input file format	Bed	Bam	Bed	Eland/sam/bed/bam
Preprocessing	Yes	Yes	No	Yes
Resolution	Single nucleotide	Cluster of reads	Genome binning	Predefined regions
Statistical model	Background estimation	Zero-Truncated Negative Binomial	Many	Background estimation
Mutation	Yes	Yes	Yes	No
FDR	Permutation	Benjamini - Hochberg	Benjamini - Hochberg	Modified FDR
Peak length assessment	User defined	Automatic	Automatic	Automatic
Annotation	No	Yes	No	No
Control data	No	Yes	Yes	No
Implementation	Perl	Python/Galaxy	Executable binary	Python