Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Apr 22;13:22. doi: 10.1186/s13072-020-00342-y

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 4 — Generalized ATAC-seq data processing workflow intended for comparative analysis. Stepwise bioinformatics process and example commands for analyzing ATAC-seq data from raw reads to calling peaks for downstream differential accessibility analysis. Consider “treat1” as an example mouse ATAC-seq Illumina paired-end library. Blue text denotes optional or conditional steps dependent on experimental design and desired output. Users seeking only to discover replicate-concordant accessible regions in a singular cell state may wish to call naïve overlapping peaks, though this step is not necessary for differential accessibility analysis. Bash scripts for Tn5 coordinate shift (bedpeTn5shift.sh), minimal BEDPE format conversion (bedpeMinimalConvert.sh), and calling naïve overlap broad peaks (naiveOverlapBroad.sh) are located in the additional files section along with a machine-readable text version of this workflow