{"id":19113107,"url":"https://github.com/carlescn/scrnaseq-tools","last_synced_at":"2026-04-12T11:51:36.845Z","repository":{"id":63917327,"uuid":"571574431","full_name":"carlescn/scRNAseq-tools","owner":"carlescn","description":"This is a set of bash wrapper scripts for STAR that simplify it's setup and use with a set of pre-defined parameters.","archived":false,"fork":false,"pushed_at":"2023-06-13T17:40:27.000Z","size":94,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-22T11:41:21.326Z","etag":null,"topics":["bash","bioinformatics","danio-rerio","linux","scrna-seq","zebrafish"],"latest_commit_sha":null,"homepage":"","language":"Shell","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/carlescn.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":"2022-11-28T12:33:13.000Z","updated_at":"2024-08-10T03:27:37.000Z","dependencies_parsed_at":"2024-11-09T04:45:43.573Z","dependency_job_id":null,"html_url":"https://github.com/carlescn/scRNAseq-tools","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/carlescn/scRNAseq-tools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carlescn%2FscRNAseq-tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carlescn%2FscRNAseq-tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carlescn%2FscRNAseq-tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carlescn%2FscRNAseq-tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/carlescn","download_url":"https://codeload.github.com/carlescn/scRNAseq-tools/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carlescn%2FscRNAseq-tools/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270278463,"owners_count":24557180,"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","status":"online","status_checked_at":"2025-08-13T02:00:09.904Z","response_time":66,"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":["bash","bioinformatics","danio-rerio","linux","scrna-seq","zebrafish"],"created_at":"2024-11-09T04:35:13.453Z","updated_at":"2026-04-12T11:51:31.823Z","avatar_url":"https://github.com/carlescn.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# scRNAseq-tools\n\n[![GPLv3 license](https://img.shields.io/badge/License-GPLv3.0-blue.svg)](https://github.com/carlescn/scRNAseq-tools/blob/main/LICENSE)\n[![made-with-bash-5.1](https://img.shields.io/badge/Made%20with-Bash%205.1-1f425f.svg?logo=gnubash)](https://www.gnu.org/software/bash/)\n[![Linux](https://img.shields.io/badge/OS-Linux-yellow.svg?logo=linux)](https://www.linux.org/)\n[![STAR-2.7.9a](https://img.shields.io/badge/STAR-2.7.10b-darkgreen.svg)](https://github.com/alexdobin/STAR)\n\n## STARsolo scripts\n\nThis is a set of bash scripts I wrote\nas a wrapper for [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md)\nto simplify it's setup\nand for running it with a set of parameters\nwhich try to replicate the output of\n[10x Genomics Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).\n\nThe scripts are located under the directory `./bin/starsolo`\n([see documentation](/bin/starsolo/README.md)):\n\n- **`starsolo-setup-linux-x86_64.sh`**:\n  downloads the [STAR executable](https://github.com/alexdobin/STAR/)\n  and the [whitelists from 10xGenomics](https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-).\n- **`starsolo-gen-idx-danio-rerio.sh`**:\ndownloads the reference genome GRCz11 for the sp. Danio_rerio\n  from [ENSEMBL](https://www.ensembl.org/Danio_rerio/Info/Index)\n  and generates the STAR genome index.\n- **`run-starsolo.sh`**:\n  runs the STARsolo algorithm with some preset parameters.\n\n## SRA scripts\n\nBecause I needed some experiment data to test the STARsolo scripts,\nI also wrote a couple of scripts\nto obtain FASTQ files from the\n[SRA repository](https://www.ncbi.nlm.nih.gov/sra/docs/).\n\nThese download the raw data files from the SRA repository\nand extract the original FASTQ files\nusing the `fastq-dump` tool from\n[SRA-toolkit](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit).\nThe obtained FASTQ files should be equivalent to the output of\n[cellranger count](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).\n\nThe scripts are located under the directory `./bin/sra`\n([see documentation](/bin/sra/README.md)):\n\n- **`get-fastq-dump.sh`:**\n  downloads the tool fastq-dump from the\n  [SRA-toolkit](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit).\n- **`sra-to-cellranger-count.sh`:**\n  downloads the raw data from the SRA repositories\n  for the given ID(s) and extracts the original FASTQ files.\n\n## Workflow example\n\nFinally,\nI provide a workflow example\n(`workflow_example.sh`)\nthat uses all these scripts to:\n\n1. Download and setup all the tools.\n1. Download some example data from the SRA repositories.\n1. Run STARsolo to obtain a cell-feature count matrix.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarlescn%2Fscrnaseq-tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcarlescn%2Fscrnaseq-tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarlescn%2Fscrnaseq-tools/lists"}