I have created a merged_BAM file by merging 100 individual bam files.
I am calling chip-seq peaks on merged_BAM file using MACS2
I want to obtain p-value threshold to filter out the MACS2 peaks
One of the ways I am doing is using IDR on 3 copies of merged_BAM that are created by randomly subsampling 33% of the original merged_BAM file.
merged_BAM_replicate 1( 33% of original merged_BAM) merged_BAM_replicate 2( 33% of original merged_BAM) merged_BAM_replicate 3( 33% of original merged_BAM)
Do you have other suggestions?