https://www.pierre-francois-roux.com/tags/peak-calling/ Recent content in Peak calling on Pierre-François Roux Hugo -- gohugo.io en-us © 2021 Pierre-François Roux Fri, 19 Jun 2026 09:20:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/use-pseudoreplicates-to-make-peak-sets-less-fragile/ Fri, 19 Jun 2026 09:20:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/use-pseudoreplicates-to-make-peak-sets-less-fragile/ Peak sets are surprisingly fragile. Change one replicate, one depth threshold or one peak-calling parameter, and thousands of regions may appear or disappear. A useful way to reduce this fragility is to ask whether peaks are reproducible under resampling. This is the logic behind pseudoreplicates and IDR-style workflows. The Core Idea For each biological replicate: Randomly split aligned reads into two pseudoreplicates. Call peaks on the original replicate. Call peaks on each pseudoreplicate.