HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif discovery and NGS analysis. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-seq, GRO-seq, RNA-seq, DNase-seq, Hi-C and numerous other types of functional genomics sequencing data sets.

Functions #

• Basic NGS analysis
  • makeBigWig.pl
  • getDifferentialPeaksReplicates.pl
  • annotatePeaks.pl
  • analyzeRNA.pl
  • analyzeRepeats.pl
  • getDiffExpression.pl
• Additional analysis
  • tagDir2bed.pl
  • bed2pos.pl
  • pos2bed.pl
  • getRandomReads.pl
  • batchParalle.pl
  • batchMakeTagDirectory.pl
  • analyzeChIP-Seq.pl
• Motif analysis
  • findMotifs.pl
  • findMotifsGenome.pl
  • scanMotifGenomeWide.pl

Examples #

ChIP-seq peaks.bed 파일로 motif 분석을 하고자 할 경우,

$ findMotifsGenome.pl peaks.bed hg19 output -size 200 -mask

위 명령을 수행하면, output 디렉토리에 분석 결과 자료가 html로 정리되어 제공된다. 찾은 motif를 유전체에서 찾아보려면,

$ scanMotifGenomeWide.pl motif-file hg19 -bed > scan.bed

위 명령을 수행하면, 해당 motif가 있는 영역이 BED 형식으로 저장된다.

만일, 찾은 motif의 타겟 유전자를 찾고 싶으면, annotatePeak.pl 프로그램을 사용한다. 위에서 찾은 motif 파일을 입력으로 넣을 수 있다.

$ annotatePeak.pl peaks.bed hg19 -m motifs.homer > peaks-anno-with-motif.tsv

이정도면, 이 프로그램 하나로 ChIP-seq 분석 왠만한 건 다 되는 듯.

Incoming Links #

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