{"id":20083769,"url":"https://github.com/y9c/m6a-sacseq","last_synced_at":"2025-05-06T01:31:39.647Z","repository":{"id":41369462,"uuid":"445675696","full_name":"y9c/m6A-SACseq","owner":"y9c","description":"🧪 Optimized protocol for m6A-SAC-seq ","archived":false,"fork":false,"pushed_at":"2023-01-30T07:14:42.000Z","size":15764,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2023-08-14T15:48:19.281Z","etag":null,"topics":["docker","epitranscriptome","epitranscriptomics","m6a","modification","ngs","pipeline","rna","sac-seq","single-base"],"latest_commit_sha":null,"homepage":"https://sacseq.chuan.science/","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/y9c.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}},"created_at":"2022-01-07T23:11:08.000Z","updated_at":"2023-06-02T22:44:26.000Z","dependencies_parsed_at":"2023-02-16T05:01:25.773Z","dependency_job_id":null,"html_url":"https://github.com/y9c/m6A-SACseq","commit_stats":null,"previous_names":[],"tags_count":3,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-SACseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-SACseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-SACseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-SACseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/y9c","download_url":"https://codeload.github.com/y9c/m6A-SACseq/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224479526,"owners_count":17318292,"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":["docker","epitranscriptome","epitranscriptomics","m6a","modification","ngs","pipeline","rna","sac-seq","single-base"],"created_at":"2024-11-13T15:48:41.611Z","updated_at":"2024-11-13T15:48:42.380Z","avatar_url":"https://github.com/y9c.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Docker](https://img.shields.io/docker/pulls/y9ch/sacseq.svg)](https://hub.docker.com/r/y9ch/sacseq)\n[![DOI:10.1038/s41587-022-01243-z](https://zenodo.org/badge/DOI/10.1038/s41596-022-00765-9.svg)](https://doi.org/10.1038/s41596-022-00765-9)\n[![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1038/s41596-022-00765-9)](https://www.nature.com/articles/s41596-022-00765-9/metrics)\n\n# m\u003csup\u003e6\u003c/sup\u003eA-SAC-seq\n\n## Overview of the workflow\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://y9c.github.io/m6A-SACseq/Introduction#gh-light-mode-only\"\u003e\n    \u003cimg src=\"./docs/scheme.svg\" /\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://y9c.github.io/m6A-SACseq/Introduction#gh-dark-mode-only\"\u003e\n    \u003cimg src=\"./docs/scheme_dark.svg\" /\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n## How to use?\n\nA [docker image](https://hub.docker.com/r/y9ch/sacseq) containing the source code and dependencies has been published for reproducibility. You can run it using the [singularity](https://sylabs.io/singularity) container runtime.\n\nThe entire analysis can be completed in just three steps:\n\n1. **Specific the path (with label) of both rawdata and references for your project in a YAML format.**\n\n   \u003cdetails\u003e\n     \u003csummary\u003e\u003ccode\u003edata.yaml\u003c/code\u003e for example\u003csup\u003e(Click to expand)\u003c/sup\u003e\u003c/summary\u003e\n\n   ```yaml\n   samples:\n     HeLa-WT:\n       input:\n         rep1:\n           - R1: ./rawdata/HeLa-WT-polyA-input-rep1-run1_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-input-rep1-run1_R2.fq.gz\n           - R1: ./rawdata/HeLa-WT-polyA-input-rep1-run2_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-input-rep1-run2_R2.fq.gz\n         rep2:\n           - R1: ./rawdata/HeLa-WT-polyA-input-rep2-run1_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-input-rep2-run1_R2.fq.gz\n           - R1: ./rawdata/HeLa-WT-polyA-input-rep2-run2_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-input-rep2-run2_R2.fq.gz\n       treated:\n         rep1:\n           - R1: ./rawdata/HeLa-WT-polyA-treated-rep1-run1_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-treated-rep1-run1_R2.fq.gz\n           - R1: ./rawdata/HeLa-WT-polyA-treated-rep1-run2_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-treated-rep1-run2_R2.fq.gz\n         rep2:\n           - R1: ./rawdata/HeLa-WT-polyA-treated-rep2-run1_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-treated-rep2-run1_R2.fq.gz\n           - R1: ./rawdata/HeLa-WT-polyA-treated-rep2-run2_R1.fq.gz\n             R2: ./rawdata/HeLa-WT-polyA-treated-rep2-run2_R2.fq.gz\n   references:\n     spike:\n       fa: ./ref/spike_expand.fa\n       bt2: ./ref/spike_expand\n     spikeN:\n       fa: ./ref/spike_degenerate.fa\n       blast: ./ref/spike_degenerate\n     rRNA:\n       fa: ./ref/Homo_sapiens.GRCh38.rRNA.fa\n       bt2: ./ref/Homo_sapiens.GRCh38.rRNA\n     smallRNA:\n       fa: ./ref/Homo_sapiens.GRCh38.smallRNA.fa\n       bt2: ./ref/Homo_sapiens.GRCh38.smallRNA\n     genome:\n       fa: ./ref/Homo_sapiens.GRCh38.genome.fa\n       star: ./ref/Homo_sapiens.GRCh38.genome\n       gtf: ./ref/Homo_sapiens.GRCh38.genome.gtf\n       gtf_collapse: ./ref/Homo_sapiens.GRCh38.genome.collapse.gtf\n     contamination:\n       fa: ./ref/contamination.fa\n       bt2: ./ref/contamination\n   ```\n\n   _Read the [documentation](https://y9c.github.io/m6A-SACseq/Run-the-pipeline.html#refer-rawdata-and-references-in-the-configuration-file) on how to customize._\n\n   \u003c/details\u003e\n\n2. **Run all the analysis by one command**:\n\n   ```bash\n   apptainer run docker://y9ch/sacseq:latest\n   ```\n\n   Note that when you storge your input file in a mounted partition, don't forget to add `--bind / -B` command to mount the partition.\n   For example, using `apptainer run -B /data docker://sacseq:latest`...\n\n    \u003cdetails\u003e\n      \u003csummary\u003edefault settings\u003csup\u003e(Click to expand)\u003c/sup\u003e\u003c/summary\u003e\n\n   - default config file: `data.yaml`\n   - default output dir: `./results`\n   - default jobs in parallel: `48`\n\n   _Read the [documentation](https://y9c.github.io/m6A-SACseq/Run-the-pipeline.html#customized-analysis-parameters) on how to customize._\n\n   \u003c/details\u003e\n\n3. **View the analytics report and use the m\u003csup\u003e6\u003c/sup\u003eA sites for downstream analysis**.\n\n   The output of all the steps will be in one folder (`./results`) under the current path. A webpage report of all the analysis will be in `./results/report.html` \u003csup\u003e([example](https://y9c.github.io/m6A-SACseq/demo_output.html))\u003c/sup\u003e.\n\n## Documentation\n\nhttps://y9c.github.io/m6A-SACseq/\n\n## Citation\n\n- Ge, R., Ye, C., Peng, Y. et al. m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nat Protoc (2022). https://doi.org/10.1038/s41596-022-00765-9\n\n\u0026nbsp;\n\n\u003cp align=\"center\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/y9c/y9c/master/resource/footer_line.svg?sanitize=true\"\n  /\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n  Copyright \u0026copy; 2021-present\n  \u003ca href=\"https://github.com/y9c\" target=\"_blank\"\u003eChang Y\u003c/a\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/y9c/m6A-SACseq/blob/master/LICENSE\"\u003e\n    \u003cimg src=\"https://img.shields.io/static/v1.svg?style=for-the-badge\u0026label=License\u0026message=GPLv3\u0026logoColor=d9e0ee\u0026colorA=282a36\u0026colorB=c678dd\" /\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fm6a-sacseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fy9c%2Fm6a-sacseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fm6a-sacseq/lists"}