Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

Biology Direct

Table 1 Comparison among FC and similar tools available in the literature

	FC	CisGenome [16]	Sole-Search [17]	[18]
Raw conversion	Yes	No	Yes	No
SOLiD data support	Yes	Not explicit	Not explicit	Not explicit
Quality control	Yes	No	No	No
Alignment	Yes (Bowtie)	No	Yes	No
Peak Calling	Yes (MACS)	Yes (SeqPeak)	Yes	Yes (PICS)
Annotation	Yes	Yes	Yes	Yes
Wiggle file	Yes	Yes	Yes	No
bigWig file	Yes	No	No	No
tdf file	Yes	No	No	No
Motif Analysis	No	Yes	No	Yes
Samples comparison	Unlimited	One pair	One pair	One pair
Handle replicates	Yes	No	Yes	No
Single package	Yes	Yes	Yes	No

ISSN: 1745-6150