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Is there an explanation for what the broad-cutoff means for broad peak calling for MACS. In the documentation for MACS they say it is a q-value cutoff for a broad peak region? I ask because in my result file, I still see peaks that have a -log10(qvalue) of less than the cutoff, so if my cutoff is 0.1 (the default), I see peaks that have a -log10(qvalue) of less than 1. Unless of course this is not what the broad-cutoff refers to? Thanks.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...