228    ◾    Bioinformatics

cut -f1,2,3,4 chip1_peaks.narrowPeak > vis/chip1_peaks.bed

cut -f1,2,3,4 chip2_peaks.narrowPeak > vis/chip2_peaks.bed

cut -f1,2,3,4 chip2_peaks.narrowPeak > vis/chip3_peaks.bed

The converted files were saved in “macs3output/vis” directory as shown in Figure 6.5. Those

files can be visualized in a genome browser. If you are working with a Linux with a graphi-

cal desktop, that works for the next step; otherwise, you can copy “macs3output” directory

including “vis” to a Windows or Mac desktop using FileZilla, which is an open-source FTP

application for file transfer, available at “https://filezilla-project.org/”. The “macs3output”

directory contains all MACS3 output files that we will use in later analyses and “vis” sub-

directory contains files for visualization in a genome browser.

In the next step, we will use a genome browser. In this exercise, we will use the IGB [8],

which is a standalone software available for Linux, Windows, and Mac OS X. It can be

downloaded from “https://www.bioviz.org/” and installed on a local computer. Once it has

been installed, open it, click “H. sapiens”, open the directory where the Wig and BED files

are stored, and for each ChIP-Seq sample, use the mouse to drag “*control_lambda.wig”,

“*treat_pileup.wig”, and “*peaks.bed” to the viewer just above “RefSeq curated (+)” track

and every time click “Load Data” button on the top right. You can also change the color of

the tracks of each sample by clicking the right button on the track and select “Customize”

from the popup menu and then choose a color (Figure 6.6).

As shown in Figure 6.6, each ChIP-Seq sample has three tracks: control (input data),

treated (ChIP-Seq), and the peaks. It is clear that the signal of input data (control) is flat but

the ChIP-Seq signals are with peaks. The peak track shows the peak position. Compare the

control signal of each sample to its corresponding treated (ChIP-Seq) signal. You can move

along the genome by using grab tool (hand icon), or zoom in and out using the horizontal

zoom slider on the top. You can also use the mouse to move left or right. The IGB comes

with search tools that can be used to search for a gene or to navigate to a specific position

in a chromosome.

Figure 6.7 shows a typical mixed (sharp and broad) signal of Poly II for the three sam-

ples after zooming in.

FIGURE 6.5  Wig and BED files ready to be visualized in a genome browser.