Averaging multiple IgG BAM files for use as a control in ChromHMM
Hello, I have three BAM files from Cut&Tag experiments using IgG (negative control). I would like to use them as a common control for several histone marks in a ChromHMM analysis. Instead of using the three BAM files separately, I want to create a single BAM file that represents the average or merged signal from the three IgG datasets to get a more robust estimate of the background. Is there any recommended method or tool to do this kind of averaging or merging directly from BAM files?
Thank you for your help
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samtools mergewill merge multiple BAM files into one --> https://www.htslib.org/doc/samtools-merge.htmlSee if Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM? helps with your question.
BAM files do not contain counts or an "average-able" metric so I would simply merge the files indeed, maybe after subsampling to the same read count to have it a bit "more fair".