homer

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing 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.

http://homer.ucsd.edu/homer/

• 加载软件

  module load homer/4.11

• 查看已下载和可下载的基因组

  Version Installed   Package Version Description
  SOFTWARE
  +   homer   v4.11.1 Code/Executables, ontologies, motifs for HOMER
  ORGANISMS
  +   zebrafish-o v6.3    Danio rerio (zebrafish) accession and ontology information
  -   ciona   v6.3    Ciona intestinalis (ciona) accession and ontology information
  -   human-o v6.3    Homo sapiens (human) accession and ontology information
  ...
  -   rice    v6.3    Oryza sativa (rice) accession and ontology information
  -   dog v6.3    Canis lupus familiaris (dog) accession and ontology information
  -   worm-o  v6.3    Caenorhabditis elegans (worm) accession and ontology information
  -   hydra   v6.3    Hydra vulgaris (hydra) accession and ontology information
  PROMOTERS
  -   human-p v5.5    human promoters (human)
  -   chicken-p   v5.5    chicken promoters (chicken)
  -   arabidopsis-p   v6.3    arabidopsis promoters (arabidopsis)
  -   rat-p   v5.5    rat promoters (rat)
  -   fly-p   v5.5    fly promoters (fly)
  -   zebrafish-p v5.5    zebrafish promoters (zebrafish)
  -   mouse-p v5.5    mouse promoters (mouse)
  -   yeast-p v5.5    yeast promoters (yeast)
  -   frog-p  v5.5    frog promoters (frog)
  -   worm-p  v5.5    worm promoters (worm)
  GENOMES
  +   danRer10    v6.4    zebrafish genome and annotation for UCSC danRer10
  -   sacCer3 v6.4    yeast genome and annotation for UCSC sacCer3
  -   panTro5 v6.4    human genome and annotation for UCSC panTro5
  -   hg17    v6.4    human genome and annotation for UCSC hg17
  -   dm6 v6.4    fly genome and annotation for UCSC dm6
  ...
  -   xenTro2 v6.4    frog genome and annotation for UCSC xenTro2
  -   ci3 v6.4    ciona genome and annotation for UCSC ci3
  -   gorGor4 v6.4    human genome and annotation for UCSC gorGor4
  -   taeGut2 v6.4    zebrafinch genome and annotation for UCSC taeGut2
  -   petMar3 v6.4    lamprey genome and annotation for UCSC petMar3
  SETTINGS
  

  其中前面有"+"的为已下载的数据，如果没有下载，则联系管理员下载

• 使用举例

  findMotifsGenome.pl tmp.bed danRer10 outputDir -len 8,10,12