Scripts for analysis of ChIP seq. Additional data for:
HP1 dimerization but not LLPS drives the condensation and segregation of H3K9me-marked chromatin. Karthik Eswara, Jennifer Semple, Francesca Rivas-Cuestas, Shakila Ali, Sonia El Mouridi, Yogesh Ostwal, Christian Frøkjær-Jensen, Peter Meister, Wolfgang Fischle doi: https://doi.org/10.1101/2025.11.13.687974
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makeSampleSheet.R - script to create input sample sheet for nf-core pipeline
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nf_chipseq_submit.sh - used to run nf-core/chipseq pipeline version 2.1.0
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gatherQCplots.py - to collect individual pdfs made by nf-core into a single file.
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averageBigwigs.sh - script using deeptools to create ip-input and log2(ip/input) tracks, as well as averaging repeats.
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prepareForDeeptools.R - script to create a file with a list of average log2(IP/input) with separate column for sample name to use as input for deeptools. Also it takes the table of consensus peaks output by nf-core/chipseq pipeline and creates bedfiles of peaks present in at least 3 replicates among all H3K9me2 ChIP seq samples, or present in all three N2 replicates.
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H3K9me2_overEM88peaks.sh - plotting H3K9me2 signal from different samples over set of consensus peaks using deeptools.