222    ◾    Bioinformatics

chp2=$(samtools view -c ENCFF000XJS_chp2_filt.bam)

fact2=$(echo “scale=6; $chp2/$inpc” | bc)

samtools view -b -s $fact2 ENCFF000XGP_inp0_filt.bam >

ENCFF000XGP_inp0_filt_inp2.bam

chp3=$(samtools view -c ENCFF000XKD_chp3_filt.bam)

fact3=$(echo “scale=6; $chp3/$inpc” | bc)

samtools view -b -s $fact3 ENCFF000XGP_inp0_filt.bam >

ENCFF000XGP_inp0_filt_inp3.bam

You can then double check the read count in the new control files for the ChIP-Seq files.

The read counts for control files are shown in Table 6.1.

samtools view -c ENCFF000XGP_inp0_filt_inp1.bam

samtools view -c ENCFF000XGP_inp0_filt_inp2.bam

samtools view -c ENCFF000XGP_inp0_filt_inp3.bam

Up to this point, we have three ChIP-Seq BAM files and three control BAM files, one for

each ChIP-Seq file. Before proceeding to the next step, you may decide to view the align-

ment in the BAM file with the “samtools tview” command or any other BAM viewing pro-

gram. When we use “samtools tview”, the “-p” option is used to specify a specific position.

To view a BAM file, you need to sort the alignments by coordinate and then index it. As an

example, we will view only one file (Figure 6.3).

samtools sort ENCFF000XJP_chp1_filt.bam -o

ENCFF000XJP_chp1_filt_so.bam

samtools index ENCFF000XJP_chp1_filt_so.bam

samtools tview \

FIGURE 6.3  Visualizing reads aligned to the reference genome using “samtools tview” command.