{"id":21134236,"url":"https://github.com/cometsong/atac_seq_nxf","last_synced_at":"2026-01-01T23:09:36.485Z","repository":{"id":141040883,"uuid":"290309044","full_name":"cometsong/ATAC_Seq_nxf","owner":"cometsong","description":"ATAC_Seq Analysis Pipeline using Nextflow framework.","archived":false,"fork":false,"pushed_at":"2020-11-12T21:39:50.000Z","size":52,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-21T06:29:05.373Z","etag":null,"topics":["atac-seq","bioinformatics","nextflow","pipeline"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cometsong.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-08-25T19:49:47.000Z","updated_at":"2020-11-12T21:39:53.000Z","dependencies_parsed_at":null,"dependency_job_id":"182c44b2-e2df-431f-99cb-fe1ca4f82d2d","html_url":"https://github.com/cometsong/ATAC_Seq_nxf","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2FATAC_Seq_nxf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2FATAC_Seq_nxf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2FATAC_Seq_nxf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2FATAC_Seq_nxf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cometsong","download_url":"https://codeload.github.com/cometsong/ATAC_Seq_nxf/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243581060,"owners_count":20314162,"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","bioinformatics","nextflow","pipeline"],"created_at":"2024-11-20T06:25:27.525Z","updated_at":"2026-01-01T23:09:36.459Z","avatar_url":"https://github.com/cometsong.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"## ATAC_Seq analysis pipeline (in Nextflow)\n\nThe Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq)\nexperiment provides genome-wide profiles of chromatin accessibility. Briefly,\nthe ATAC-seq method works as follows: loaded Tn5 transposase inserts sequencing\nprimers into open chromatin sites across the genome, and reads are then\nsequenced. The ends of the reads mark open chromatin sites.\n\nThe developed pipeline maps trimmed paired-end Illumina reads from mouse\nstrains, to strain specific references. Mapped reads are then filtered to remove\nduplicates, mitochondrial reads, and reads that are not properly paired. Reads\nare shifted 4 bp to the right and reads on the negative strands should be\nshifted 5 bp to the left to accommodate   Tn5 cut positioning. Peaks are then\ncalled with Macs2, and sequence coverage (depth) under peaks is then calculated.\n\nQuality control metrics are also calculated. Trimmed read statistics, mapping\nstatistics, percent mitochondrial DNA, percent duplication, insert size\nestimation, library complexity statistics, and fraction of reads in peak.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fatac_seq_nxf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcometsong%2Fatac_seq_nxf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fatac_seq_nxf/lists"}