A question about analyzing MACS2 outputs
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3.0 years ago

Hi! I am new to DRIP-seq analysis and have a question about different output files, I am using MACS2 for peak calling and use DROPA to analyze the MACS2 result. I am using MACS2 in a broad peak mode, with the default parameters and this results in three output files: gappedPeak, broadPeak and a peaks.xls file. I am not exactly sure which one should I use for the downstream analysis for DROPA. I was suggested that for DRIP-seq analysis I should use broad peaks, so I went with the broadPeak file and it gave seemingly good results. But at the same time I am having a hard time understanding the difference between the peak.xls and the broadPeak files. Which one should I use for DROPA?

broad-peak dropa drip-seq macs2 • 654 views

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