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Hi Folks,
I am trying to use macs2 to call peaks then utilize idr2 to identify the final peak list. I have three biological replicates, 2 PE and 1 SE, and a target gene KO control which is SE. When performing the peak calling, I can easily input the format for the input files as -f BAM or BAMPE for each replicate, but what about when generating the concatenated peak list required to supply a peak-list for idr2. The concatenated alignment is generated by using Bowtie2 and using -1 biorep1-1,biorep2-1 -2 biorep1-2,biorep2-2 -U biorep3 to align all three replicates into a single file. How should I designate the format for this concatenated file in macs2? When generating this concatenated peak list I am not using the macs2 model build, but rather the half-size from spp.
Are there any other concerns that I should have combining PE and SE alignments?
I am trying to use macs2 to call peaks then utilize idr2 to identify the final peak list. I have three biological replicates, 2 PE and 1 SE, and a target gene KO control which is SE. When performing the peak calling, I can easily input the format for the input files as -f BAM or BAMPE for each replicate, but what about when generating the concatenated peak list required to supply a peak-list for idr2. The concatenated alignment is generated by using Bowtie2 and using -1 biorep1-1,biorep2-1 -2 biorep1-2,biorep2-2 -U biorep3 to align all three replicates into a single file. How should I designate the format for this concatenated file in macs2? When generating this concatenated peak list I am not using the macs2 model build, but rather the half-size from spp.
Are there any other concerns that I should have combining PE and SE alignments?