{"id":19434422,"url":"https://github.com/likelet/rnaseqpipe","last_synced_at":"2025-06-17T03:36:51.436Z","repository":{"id":86650917,"uuid":"145065737","full_name":"likelet/RNAseqPipe","owner":"likelet","description":"Nextflow based RNA-seq analysis pipeline","archived":false,"fork":false,"pushed_at":"2021-11-19T08:13:13.000Z","size":134,"stargazers_count":3,"open_issues_count":0,"forks_count":6,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-22T00:18:49.073Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Perl","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/likelet.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-08-17T03:11:19.000Z","updated_at":"2023-07-02T14:53:59.000Z","dependencies_parsed_at":null,"dependency_job_id":"397379f5-9e84-4145-95b3-56f9276614a9","html_url":"https://github.com/likelet/RNAseqPipe","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/likelet/RNAseqPipe","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FRNAseqPipe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FRNAseqPipe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FRNAseqPipe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FRNAseqPipe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/likelet","download_url":"https://codeload.github.com/likelet/RNAseqPipe/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FRNAseqPipe/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260286467,"owners_count":22986596,"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":[],"created_at":"2024-11-10T14:46:22.720Z","updated_at":"2025-06-17T03:36:51.415Z","avatar_url":"https://github.com/likelet.png","language":"Perl","readme":"# SYSUCC-RNAseqPipe\n\n### Quick start  for reproductive analysis \n\n    nextflow run RNAseqPipe/main.nf -profile c2 --read \"*_{1,2}.fq.gz\" --designfile \"design.file\" --comparefile \"compare.txt\"\n\n### Documentation\nThe SYSUCC-RNAseqPipe pipeline comes with documentation about the pipeline, found in the `docs/` directory:  \n\nplease find the information in [wiki](https://github.com/likelet/RNAseqPipe/wiki)  \n\n1. [Installation and configuration](docs/Installation.md)\n2. [Running the pipeline](docs/usage.md)\n3. [Output and how to interpret the results](docs/output.md)\n\n\n\n### Dependencies \n* Softwares \n    * [fastp](https://github.com/OpenGene/fastp)\n    * [STAR](https://github.com/alexdobin/STAR)\n    * [RSEM](https://deweylab.github.io/RSEM/)\n    * [Qualimap](http://qualimap.bioinfo.cipf.es/)\n    * [DAtools](https://github.com/likelet/DAtools)\n    * [MultiQC](https://github.com/ewels/MultiQC)\n    * [GSEA](http://software.broadinstitute.org/gsea/index.jsp)  \n    * Several R packages for downstream analysis.\n\n### Input file  \n\n* `design.txt`  \nsampleInfor presents the experimental design of your data set, it is just like a design file of `DESeq2` and `EdgeR` input.  \n\n        Sample\tType\n        P1003NA\tN\n        P1003TA\tT\n        P1162NA\tN\n        P1162TA\tT\n        P1408NA\tN\n        P1408TA\tT\n        P1527NA\tN\n        \n* `compare.txt`\nspecify which group to compare in your differential expression analysis \n        \n        T_vs_N\n       \n`T` and `N` are the identical strings as the `Type` column in `design.txt`.\n\n\n### command parameters \n\n\n\n* `--reads`  \n    \n    suffix of your raw reads file. For example, `*_{1,2}.fq.gz` for paired end reads file `sampleA_1.fq.gz` and `sampleA_2.fq.gz `  \n    \n* `--designfile`  \n    \n    design file  \n    \n* `--comparefile`  \n    \n    compare file \n    \n* `--gene_gtf`  \n    \n    gtf file for building your STAR index \n\n* `--singleEnd`  \n    \n    `true` when using a single End reads input, default `false` \n\n* `--strand`  \n    \n    `true` when using strand specific library , default `false` \n     \n* `--skip_qc`   \n\n    set `ture` if you are going to skip qc step \n    \n* `--without_replicate`   \n\n    set `ture` if your have no biological replicate.       \n    *note: for no replicate mode, the compare file should be directly specified as `SampleName_vs_SampleName` have just been trimmed by `read` suffix string *  \n    \n# Credits \n* Main author:\n  * Qi Zhao ([@qi_likelet](https://github.com/likelet/))\n* Contributors:\n  * Xiaolong Zhang\n  * Kaiyu \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Frnaseqpipe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Frnaseqpipe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Frnaseqpipe/lists"}