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ChIP-seq computational analysis

CL Cecilia B. Levandowski
TJ Taylor Jones
MG Margaret Gruca
SR Sivapriya Ramamoorthy
RD Robin D. Dowell
DT Dylan J. Taatjes
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All ChIP-seq data were processed (mapped and quality checked) using a Nextflow pipeline, ChIP-Flow v1.0 (https://github.com/Dowell-Lab/ChIP-Flow). A full pipeline report of the run as well as a quality control report generated by MultiQC (v. 1.7), including trimming, mapping, coverage, and complexity metrics are included in S6 Table. Peak calls were generated using MACS2 narrowPeak. The q-value default cutoff was also decreased from the default of 0.05 to 1e-5. Blacklisted regions (those having artificially high signal and read mapping, http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human) were removed using BEDTools intersect [82]. PyGenomeTracks [83] was used to generate track images.

Copyright and License information:  ©2021 Levandowski et al
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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