{"id":21644809,"url":"https://github.com/gagneurlab/fraser-analysis","last_synced_at":"2025-04-11T18:33:37.559Z","repository":{"id":95736168,"uuid":"229213837","full_name":"gagneurlab/FRASER-analysis","owner":"gagneurlab","description":"Accompanying analysis code for the FRASER manuscript","archived":false,"fork":false,"pushed_at":"2020-08-27T05:28:59.000Z","size":4893,"stargazers_count":26,"open_issues_count":7,"forks_count":7,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-25T14:38:46.251Z","etag":null,"topics":["outlier-detection","r","rare-disease","rna-seq","snakemake","workflow"],"latest_commit_sha":null,"homepage":"https://tinyurl.com/FRASER-paper","language":"R","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/gagneurlab.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":"2019-12-20T07:32:24.000Z","updated_at":"2024-11-02T19:50:36.000Z","dependencies_parsed_at":"2023-04-24T17:01:21.115Z","dependency_job_id":null,"html_url":"https://github.com/gagneurlab/FRASER-analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FFRASER-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FFRASER-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FFRASER-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gagneurlab%2FFRASER-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gagneurlab","download_url":"https://codeload.github.com/gagneurlab/FRASER-analysis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248459067,"owners_count":21107217,"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":["outlier-detection","r","rare-disease","rna-seq","snakemake","workflow"],"created_at":"2024-11-25T05:42:42.624Z","updated_at":"2025-04-11T18:33:37.552Z","avatar_url":"https://github.com/gagneurlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FRASER-analysis\n\nThis is the accompanying analysis repository of the paper:\n\n`Detection of aberrant splicing events in RNA-seq data with FRASER`. \n\nThe paper can be found [on bioRxiv](https://www.biorxiv.org/content/10.1101/2019.12.18.866830v1).\n\nThis repository contains the full pipeline and code to reproduce the results published in the paper using [snakemake](https://snakemake.readthedocs.io/en/stable/) and [wBuild](https://github.com/gagneurlab/wBuild). \n\n## Project structure\n\nThis project is setup as a [wBuild workflow](https://github.com/gagneurlab/wBuild). This is an automatic build tool for R reports based on [snakemake](https://snakemake.readthedocs.io/en/stable/).\n\n* The `wbuild.yaml` is the main configuration file to setup up the workflow\n* The `Scripts` folder contains scripts which will be rendered as HTML reports\n* The `src` folder contains additional helper functions and scripts\n* The `Output` folder will contain all files produced in the analysis pipeline\n    * `Output/data` has all raw RDS output files\n    * `Output/html` contains the final HTML report\n    * `Output/paper_figures` has all paper figures\n\n## Data and prerequisites \n\nThis project depends on the python package `wBuild` and the R package `FRASER`. Further, we use the [Leafcutter](https://github.com/davidaknowles/leafcutter) adaptation used in the [Kremer et al paper](https://www-nature-com.eaccess.ub.tum.de/articles/ncomms15824), which can be found [here](https://i12g-gagneurweb.in.tum.de/gitlab/mertes/rare-disease-leafcutter).\n\nThe pipeline starts with the raw aligned GTEx samples V7P and their genotype calls, which can be downloaded from [dbGaP](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v7.p2). Since the data are not publicly shareable one has to apply for the data at [dbGaP]( https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v6.p1). \n\n## Repository setup\n\nFirst download the repo and its dependencies:\n\n```\n# R package used throughout the workflow\ngit clone https://github.com/gagneurlab/FRASER\ngit clone https://i12g-gagneurweb.in.tum.de/gitlab/mertes/rare-disease-leafcutter\n\n# download needed SRA annotation db\nwget -O - 'https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz' | gunzip -c \u003e 'Data/filemapping/SRAmetadb.sqlite'\n\n# analysis code\ngit clone https://github.com/gagneurlab/FRASER-analysis\ncd FRASER-analysis\n```\n\nand install wbuild using pip by running.\n\n```\npip install wBuild\nwBuild init\n```\n\nSince `wBuild init` will reset the current `Snakefile`, ` readme.md`, and `wbuild.yaml` we have to revert them again with git.\n\n```\ngit checkout Snakefile\ngit checkout wbuild.yaml\ngit checkout readme.md\n```\n\nTo make sure all packages needed in the analysis are installed source the following file in R\n\n```\nRscript ./src/r/install_dependencies.R\n```\n\n## Run the full pipeline\n\nTo run the full pipeline, execute the following command with 10 jobs and maximum 40 cores in parallel:\n\n```\n# init datasets to be used\nsnakemake -j 25 --cores 25 defineDatasets\n\n# run full analysis on datasets\nsnakemake -j 10 --cores 40 Output/paper_figures/supplement_final.pdf\n```\n\nor to run it on the cluster with SLUM installed: \n\n```\nsnakemake -k --restart-times 2 --cluster \"sbatch -N 1 -n 10 --mem 80G\" --jobs 20\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgagneurlab%2Ffraser-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgagneurlab%2Ffraser-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgagneurlab%2Ffraser-analysis/lists"}