{"id":48624121,"url":"https://github.com/becavin-lab/meripseq","last_synced_at":"2026-04-09T04:12:55.279Z","repository":{"id":98165607,"uuid":"191582450","full_name":"becavin-lab/MeRIPSeq","owner":"becavin-lab","description":"MeRIP-Seq pipeline analysis for m6a methylation site detection","archived":false,"fork":false,"pushed_at":"2019-06-12T14:05:13.000Z","size":159,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-09T14:32:21.622Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/becavin-lab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-06-12T14:01:50.000Z","updated_at":"2024-01-15T08:20:17.000Z","dependencies_parsed_at":"2023-05-03T09:46:49.861Z","dependency_job_id":null,"html_url":"https://github.com/becavin-lab/MeRIPSeq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/becavin-lab/MeRIPSeq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/becavin-lab%2FMeRIPSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/becavin-lab%2FMeRIPSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/becavin-lab%2FMeRIPSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/becavin-lab%2FMeRIPSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/becavin-lab","download_url":"https://codeload.github.com/becavin-lab/MeRIPSeq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/becavin-lab%2FMeRIPSeq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31585091,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-08T14:31:17.711Z","status":"online","status_checked_at":"2026-04-09T02:00:06.848Z","response_time":112,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2026-04-09T04:12:55.174Z","updated_at":"2026-04-09T04:12:55.270Z","avatar_url":"https://github.com/becavin-lab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MeRIP-Seq pipeline analysis\n\nAuthor: Christophe Bécavin, Anne Biton, Hub Bioinformatic and Biostatistic\n\n28 rue du Docteur Roux, Institut Pasteur, Paris\n\nPrevious repository: https://gitlab.pasteur.fr/cbecavin/MeRIPSeq/\n\nExecutable (2 versions are available one for local computing, another for slurm cluster computing)\n### For local analysis\n\n`sh run.sh project_name`\n\nFor example: sh run.sh Liver\n\n### For Slurm cluster\n\n`nohup ./RunSlurmExample.sh \u003e runServer.log 2\u003e\u00261 \u0026`\n\nRunSlurmExample.sh should be executable `chmod 777 RunSlurmExample.sh`\n\n## PARAMETERS:\n\nproject-name   -  Name of the project\n\nThe list of file should be in your_folder/Exp_Design/project_name_exp_design.txt\nYour sequencing data should be in : your_folder/RNASeq_raw/\nour experiment design file should be a tab-separated table with at least 5 columns:\n\n|DataName|\tIP_dataset|\tInput_dataset|\tBioCond|\tSeq|\n| ------ | ------ | ------ | ------ | ------ |\n|Am_ZT3_1|\tAm_ZT3_IP_1|\tAm_ZT3_Input_1|\tAm|\t1|\n|Am_ZT13_1|\tAm_ZT13_IP_1|\tAm_ZT13_Input_1|\tAm|\t2|\n|CONV_ZT3_1|\tCONV_ZT3_IP_1|\tCONV_ZT3_Input_1|\tCONV|\t1|\n|CONV_ZT13_4|\tCONV_ZT13_IP_4|\tCONV_ZT13_Input_4|\tCONV|\t2|\n\n(See example/Liver_exp_design.txt)\n\n## PIPELINE Description:\n\nSetup true or false each step of the workflow to run it or not\n\nINSTALL first all dependencies: See INSTALL.txt\n\n1 - setup.sh - Prepare Analysis by creating all necessary folders\n\n2 - genome.sh - Prepare genome sequence, annotation, and windows for peak detection\n\n### Run on every dataset:\n\nWARNING - Steps 3 to 7 are run separately for each datasets.\n\nWARNING - They might take a ot of time to perform, so they can be parallelized on a cluster.\n\n3 - Trimming, mapping, BAM file filtering and quality control, And WIG calculation for peak detection\n\n4 - Calculate SeqDepth for peak detection techniques\n\n5 - HTSeq - Count number of reads per genes\n\n6 - coverage_window.py - Count number of reads per window\n\n7 - peak_detection.py - Run Fisher, POI,and RPMF peak detection techniques\n\n8 - MACS2 - Run MACS2 peak detection\n\n### Run only one time per project_name\n\n9 - Search for median coverage for max coverage search\n\n10 - MultiQC for quality control\n\n11 - finalize peak detection by filtering out \"bad\" peaks, searchning for max coverage and peak center\n\n12 - (Optionnal) Annotate all peaks from all different techniques\n\n13 - Search max coverage of every peaks and center peak position on it.\n\n14 - Regroup peaks from all the detection techniques, annotate them, find overlap position with genes and referent MeRIP-Seq, CLIPSeq and TREW\n\n### Run on every dataset:\n\n15 - HTSeq - Count number of reads in each methylation sites detected\n\n### Run only one time per project_name\n\n16 - Perform differential methylation sites analysis in R\n\n17 - Run differential splicing events\n\n18 - Run Motif presence algorithm\n\n19 - Run GuitarPlot for every list of peak\n\n20 - (Optional) Compare two peak lists to Ref peaks\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecavin-lab%2Fmeripseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecavin-lab%2Fmeripseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecavin-lab%2Fmeripseq/lists"}