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Table 1 Current typical platforms for ChIP-Seq analysis

From: CSA: a web service for the complete process of ChIP-Seq analysis

Platform

system

installation

Interface

Functions & tools

workflow

Mapping

Quality control

Peak calling

Format convert

Data visualization

Find motifs

GO analysis

Peaks annotation

Pathway analysis

HOMER[22]

UNIX LINUX MacOS

Perl installation scripts

Command line

–

–

makeTagDirectory

findPeaks

pos2bed.pl,bed2pos.pl

–

findMotifsGenome.pl

annotatePeaks.pl

annotatePeaks.pl

–

ChIPSeqWorkflow[27]

UNIX LINUX

compilation from source installer

Command line

–

bowtie

–

MACS

Samtools,Bedtools

–

MEME

–

–

GAGE

ChIPseeker[23]

UNIX LINUX

R package manager

GUI/Command line

√

–

ChIPseeqerReadCountDistribution

ChIPseeqer

–

peaks coverage

ChIPseeqerFIRE,ChIPseeqerMotifMatch

–

ChIPseeqerAnnotate

iPAGE

CisGenome[28]

no limitation

compilation from source installer (for Windows)

GUI/command line

–

–

–

tilemapv2

file_bed2cod,fasta_soft2hardmask, etc.

–

motifmap_matrixscan_genome,etc.

refgene_getnearestgene

–

–

ChIP-Seq tool[29]

no limitation/UNIX LINUX

not needed

Web server/Command line

–

Chipcor,Chipextract,chipscore

–

Chippeak, chippart

Compactsga,featreplace, etc.

–

–

–

–

–

Nebula[24]

no limitation

not needed

Web server

√

Bowtie

FASTQC

HMCan,MICSA,MACS,PeakSplitter,CCAT,FindPeaks

Samtools,Bamtools

–

ChIPmunk,AhoPro

Get peak distribution around TSS/histone

√

–

ChIPseek[25]

no limitation

not needed

Web server

–

–

–

HOMER

BEDTools

peak location distribution

HOMER

√

–

KEGG

CSA

no limitation

not needed/compilation from script

Web server/local web server

√

BWA, Bowtie, Bowtie2, SOAP,BLAST,Subread,NGM

deepTools

MACS,MACS2,PeakSeq,PeakRanger,SICER, PePr,BCP,diffReps,SISSRs, FindPeaks, AREM, Fseq, BroadPeak

Samtools, bamCoverage

Mapping results,peak calling results,motif finding, Go annotation,pathway analysis

findMotifsGenome.pl

annotatePeaks.pl

annotatePeaks.pl

iPAGE