{"id":13773750,"url":"https://github.com/reskejak/ATAC-seq","last_synced_at":"2025-05-11T06:30:39.955Z","repository":{"id":41092823,"uuid":"127433398","full_name":"reskejak/ATAC-seq","owner":"reskejak","description":"Basic workflow for ATAC-seq analysis","archived":false,"fork":false,"pushed_at":"2022-01-14T13:45:27.000Z","size":126,"stargazers_count":54,"open_issues_count":3,"forks_count":27,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-02-14T03:31:30.240Z","etag":null,"topics":["atac-seq","r","shell","unix"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/reskejak.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-03-30T13:50:43.000Z","updated_at":"2024-01-19T18:13:21.000Z","dependencies_parsed_at":"2022-07-30T21:08:10.856Z","dependency_job_id":null,"html_url":"https://github.com/reskejak/ATAC-seq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/reskejak%2FATAC-seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/reskejak%2FATAC-seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/reskejak%2FATAC-seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/reskejak%2FATAC-seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/reskejak","download_url":"https://codeload.github.com/reskejak/ATAC-seq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225017837,"owners_count":17407837,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["atac-seq","r","shell","unix"],"created_at":"2024-08-03T17:01:19.729Z","updated_at":"2024-11-17T08:31:30.968Z","avatar_url":"https://github.com/reskejak.png","language":"R","funding_links":[],"categories":["DNase, ATAC, and ChIP-seq"],"sub_categories":["Normalization Methods"],"readme":"# ATAC-seq\n\nThese scripts correspond to a (differential) ATAC-seq analysis workflow as described in [our recent report](https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00342-y). It is largely based on the pipeline developed by [Anshul Kundaje's group (Stanford) and the ENCODE project](https://www.encodeproject.org/pipelines/ENCPL792NWO/).\n\nIf you use this methodology, please cite the following paper along with corresponding pipeline dependencies:\n\nJake J. Reske, Mike R. Wilson, and Ronald L. Chandler. 2020. ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation. *Epigenetics \u0026 Chromatin* **13**: 22.\n\nAttempt to run each command individually or in blocks after editing to match your own data architecture.\n\n### ATACseq_workflow.txt\n**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.\n\n![foo](https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13072-020-00342-y/MediaObjects/13072_2020_342_Fig4_HTML.png)\n\n### csaw_workflow.R\n***csaw* workflow for multiple differential accessibility analyses in R.** Consider an experimental design with *n* = 2 biological replicates from two conditions: “treat” and “control”. Describes implementation of two possible normalization methods and use of either *MACS2* peaks or *de novo* locally enriched windows as query regions for output comparison; see [*csaw* manual](https://bioconductor.org/packages/release/bioc/html/csaw.html) for additional normalization frameworks. ***Note: updates to the behavior of certain csaw functions have required slight compatibility changes to the commands described graphically, so please reference the latest R script.***\n\n![foo2](https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13072-020-00342-y/MediaObjects/13072_2020_342_Fig6_HTML.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freskejak%2FATAC-seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freskejak%2FATAC-seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freskejak%2FATAC-seq/lists"}