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When to account for the blacklisted genomic regions in ChIP-seq data analyses?

I filtered my bams out of curiosity. I had around 500 peaks before filtering. When i called on the filtered bams, i lost 100 (from the blacklist) and gained 38. The peak call was using macs2. Looking ...
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Error while running computeMatrix command in Deeptools

It worked, I installed a the newer version of deeptools, from GitHub:

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