I have two replicates of chip-seq data. And I run bowtie and call peaks using MACS separately.
MACS2 callpeak -t R1.bam -c Input1.bam -f BAM -g dm -n macs2_R1 -s 50 --call-summits --bw 151 MACS2 callpeak -t R2.bam -c Input2.bam -f BAM -g dm -n macs2_R2 -s 50 --call-summits --bw 149
Now I want to combine them together for further analysis.
Do I need to normalize them before combine together? I put input when running MACS, I thought MACS has done normalization when calling peaks.
If I should do normalization firstly, and people always say "Normalization by sequencing depth (i.e. total read count)" or "divided by total reads". How to do this? I don't have "total reads" after running thru MACS.
How can I do to combine these two sets of peaks?