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chipseq_analysis.md

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##ChIP-seq analysis pipeline

###Input files

  • BAM file for each sample (From green center pipeline)
  • BigWig file for each sample (From green center pipeline)
  • Peak bed file for each sample (From green center pipeline)
  • Design file
  • Genome annotation files (including TSS, TTS, gene region bed files)
  • Flanking length (length to extend TSS or TTS)

###Modules that can be processed parallel

####deeptTools

#Compute matrix using bigwig
computeMatrix reference-point -S bigwig_file -R Genome_range_bed_file -out matrix_file

#Draw region signal heatmap， profiles
plotHeatmap -m matrix_file --out heatmap.pdf
plotProfile -m matrix_file --out profiles.pdf

#Plots the read/fragment coverage of one or more sets of regions
plotEnrichment -b file1.bam file2.bam --BED peaks.bed -o enrichment.png

####DiffBind

#Input is design file, R package will need bam files and peak bed files
R CMD run_diffbind.R design.txt

####ChIPSeeker

R CMD run_chipseeker.R

###Output files

  • Signal heatmap around TSS, gene body and TTS
  • Genomic signal correlation PCA plots
  • Peak correlation heatmap
  • Annotation figures for peaks
  • Differential peaks results (xls files)
  • Annotation for differential peaks