/for_chip-seq

chip-seq-pipeline

Primary LanguagePython

ChIP-Seq pipeline

Motif Analysis

  • Script: motifAnalysis.py
  • Usage:

python motifAnalysis.py -p peakBEDfile -o OutputDir -n Name -g genome -find -annotate

python motifAnalysis.py -p ctcf_narrowPeak -o ctcf_results -n ctcf -g hg19 -find -annotate
  • Output: name_motif1.bed : bed file of motif in each peak region, including position, strand specific information. name_motif1_annoPeak.txt: bed file of each peak. Result format information can be found here "Finding Instance of Specific Motifs"