PT  - JOURNAL ARTICLE
AU  - Gaspar, John M.
TI  - Improved peak-calling with MACS2
AID  - 10.1101/496521
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 496521
4099  - http://biorxiv.org/content/early/2018/12/17/496521.short
4100  - http://biorxiv.org/content/early/2018/12/17/496521.full
AB  - The computational analyses of genome-enrichment assays, such as ChIP-seq and ATAC-seq, are typically concluded with a peak-calling program that identifies genomic regions that are significantly enriched. The most popular peak-caller, MACS2, assumes that the input alignment files are for single-end sequence reads by default, yet those with paired-end Illumina sequence data frequently use this default setting. This leads to erroneous coverage values and suboptimal peak identification. However, using the correct paired-end mode can introduce another set of artifacts. After thoroughly reviewing the MACS2 source code, we have modified it to limit these and other problems. Our updated version is freely available (https://github.com/jsh58/MACS).