224    ◾    Bioinformatics

the display of continuous-valued data in a track in genome browsers like UCSC Genome

Browser or Integrated Genome Browser (IGB), and “--outdir” specifies the directory where

the output files are saved.

cd ..

mkdir macs3output

macs3 callpeak \

-t bam/ENCFF000XJP_chp1_filt.bam \

-c bam/ENCFF000XGP_inp0_filt_inp1.bam \

-f BAM \

-g hs \

-n chip1 \

-q 0.05 \

--bdg \

--outdir macs3output

macs3 callpeak \

-t bam/ENCFF000XJS_chp2_filt.bam \

-c bam/ENCFF000XGP_inp0_filt_inp2.bam \

-f BAM \

-g hs \

-n chip2 \

-q 0.05 \

--bdg \

--outdir macs3output

macs3 callpeak \

-t bam/ENCFF000XKD_chp3_filt.bam \

-c bam/ENCFF000XGP_inp0_filt_inp3.bam \

-f BAM \

-g hs \

-n chip3 \

-q 0.05 \

--bdg \

--outdir macs3output

Several output files for each ChIP-Seq data have been saved in the specified output ­directory

as shown in Figure 6.4. The description of these MACS3 output files is as follows:

Excel file: The “*_peaks.xls” is an Excel file, which is the most important file that con-

tains header information in the beginning of the file and information about the peaks

called by MACS3 in nine columns. These columns are Chromosome name (chr), start posi-

tion of peak (start), end position of peak (end), length of peak region (length), absolute peak

summit position (abs_summit), pileup height at peak summit (pileup), -log10(pvalue) for

the peak summit (-log10(pvalue)), fold enrichment for this peak summit against random

Poisson distribution with local lambda (fold_enrichment), -log10(qvalue) at peak summit

(-log10(qvalue)), and name.

BedGraph format: The “*_treat_pileup.bdg” contains the peak enrichment signal and

“*_control_lambda.bdg” contains local biases for each location in the reference genome.