{"id":19162968,"url":"https://github.com/hernanmd/hisat2_bovine","last_synced_at":"2026-05-13T20:34:27.149Z","repository":{"id":71141040,"uuid":"123198843","full_name":"hernanmd/hisat2_bovine","owner":"hernanmd","description":"Scripts to index and align Bovine genome with HISAT2","archived":false,"fork":false,"pushed_at":"2018-05-22T16:15:13.000Z","size":13910,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-22T22:42:07.191Z","etag":null,"topics":["bash","bioinformatics","featurecounts","genome","genome-alignment","gff3","hisat2"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/hernanmd.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}},"created_at":"2018-02-27T22:55:36.000Z","updated_at":"2022-11-22T02:32:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"5bdea4db-2e83-49bc-bea2-486c739fb912","html_url":"https://github.com/hernanmd/hisat2_bovine","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/hernanmd/hisat2_bovine","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2Fhisat2_bovine","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2Fhisat2_bovine/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2Fhisat2_bovine/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2Fhisat2_bovine/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hernanmd","download_url":"https://codeload.github.com/hernanmd/hisat2_bovine/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2Fhisat2_bovine/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32999514,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-13T13:14:54.681Z","status":"ssl_error","status_checked_at":"2026-05-13T13:14:51.610Z","response_time":115,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bash","bioinformatics","featurecounts","genome","genome-alignment","gff3","hisat2"],"created_at":"2024-11-09T09:13:44.268Z","updated_at":"2026-05-13T20:34:27.133Z","avatar_url":"https://github.com/hernanmd.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Description\n\nScripts to index and align Bovine genome with HISAT2\n\nThe scripts in this repository enables to index and align a Bovine NGS dataset with the UMD3.1.1 Bovine Genome\n\n# Details\n\nBefore running, please open the scripts and customize for the amount of cores (threads) in your platform.\n\n## make_bgumd31.sh\n\nUse the script to index the UMD3.1.1 Bovine Genome with the HISAT2 software.\n\n## run_Hisat2.sh\n\nUse the script to map the cleaned reads with the genome index built from the previous script.\n\n## install_ReSeQC.sh\n\nUse the script if installing ReSeQC in the officially documented way does not work. The script assumes nothing about the target destination, except being a Debian-compatible Linux distribution. It requires root privilege to install dependencies.\n\n## fix_gtfFields.sh\n\nUse this script if running featureCounts results in the following message:\n\n\u003e Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file.\n\u003e The specified gene identifier attribute is 'gene_id'\n\u003e The attributes included in your GTF annotation are 'transcript_id \"rna...\";'\n\nThe script removes all rows without the gene_id annotation in the last field of a GTF record.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhernanmd%2Fhisat2_bovine","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhernanmd%2Fhisat2_bovine","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhernanmd%2Fhisat2_bovine/lists"}