Chromatin Immunoprecipitation Sequencing    ◾    227

chip1_control_lambda.bdg hg19.chrom.sizes \

vis/chip1_control_lambda.bw

bedGraphToBigWig \

chip2_control_lambda.bdg hg19.chrom.sizes \

vis/chip2_control_lambda.bw

bedGraphToBigWig \

chip3_control_lambda.bdg hg19.chrom.sizes \

vis/chip3_control_lambda.bw

#Convert *treat_pileup.bdg from bedGraph to BigWig

bedGraphToBigWig \

chip1_treat_pileup.bdg \

hg19.chrom.sizes \

vis/chip1_treat_pileup.bw

bedGraphToBigWig \

chip2_treat_pileup.bdg \

hg19.chrom.sizes \

vis/chip2_treat_pileup.bw

bedGraphToBigWig \

chip3_treat_pileup.bdg \

hg19.chrom.sizes \

vis/chip3_treat_pileup.bw

#Convert control_lambda.bw from Bigwig to wig

bigWigToWig \

vis/chip1_control_lambda.bw \

vis/chip1_control_lambda.wig

bigWigToWig \

vis/chip2_control_lambda.bw \

vis/chip2_control_lambda.wig

bigWigToWig \

vis/chip3_control_lambda.bw \

vis/chip3_control_lambda.wig

#Convert chip1_treat_pileup.bw from Bigwig to wig

bigWigToWig \

vis/chip1_treat_pileup.bw \

vis/chip1_treat_pileup.wig

bigWigToWig \

vis/chip2_treat_pileup.bw \

vis/chip2_treat_pileup.wig

bigWigToWig \

vis/chip3_treat_pileup.bw \

vis/chip3_treat_pileup.wig

We need also to modify the BED file “peaks.narrowPeak” by keeping only columns 1–4.