I am trying to do the same experiment on a sample firstly, wholly and then on a specific chromosome location of the sample.
My peak calling code is;
macs2 callpeak -t input.bam -c control.bam -g hs -f BAM --bdg --outdir /directory -n peakcall_samplename
I run it on my regular .bam files. Thank I run this code on the same .bam files(both sample and input);
samtools index era_nt_filtered_sorted.bam.bam
Second, extract chromosome region;
samtools view -b -h input.bam chr1:125000000-249250621 > input_1q.bam
And then again;
macs2 callpeak -t input_1q.bam -c control_1q.bam -g hs -f BAM --bdg --outdir /directory -n peakcall_samplename_1q
However, when I count the peaks(wc -l .narrowPeak), I see that I lost almost 25% of the peaks in the file that has less peaks and 45% of the peaks in the file that has 40x more peaks than the first one, normally. Why could be the reason for that?
Thank you so much in advance.