{"id":20425029,"url":"https://github.com/databio/ericscript","last_synced_at":"2025-04-12T18:54:22.946Z","repository":{"id":86287781,"uuid":"134263207","full_name":"databio/ericscript","owner":"databio","description":"Chimeric transcript discovery","archived":false,"fork":false,"pushed_at":"2018-05-25T15:52:32.000Z","size":1199,"stargazers_count":8,"open_issues_count":5,"forks_count":2,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-03-26T13:11:22.356Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/databio.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":"2018-05-21T12:00:46.000Z","updated_at":"2023-01-06T08:06:44.000Z","dependencies_parsed_at":"2023-03-09T06:30:35.023Z","dependency_job_id":null,"html_url":"https://github.com/databio/ericscript","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/databio%2Fericscript","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fericscript/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fericscript/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fericscript/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/ericscript/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248618262,"owners_count":21134200,"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":"2024-11-15T07:12:03.816Z","updated_at":"2025-04-12T18:54:22.928Z","avatar_url":"https://github.com/databio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## EricScript Readme v2.1 (Feb 2016)\nPlease feel free to email the author if you have any questions or issues.\nmatteo.benelli AT gmail.com\n\n### INFORMATION\nEricScript is a software package developed in R, perl and bash scripts.\nEricScript uses the BWA aligner to perform the mapping on the transcriptome reference and samtools to handle with SAM/BAM files. Recalibration of the exon junction reference is performed by using BLAT.\n\n\n### REQUIREMENTS\nDownload and install R: http://cran.r-project.org/\nDownload and install the \"ada\" R package: http://cran.r-project.org/web/packages/ada/index.html\nDownload and install BWA: http://bio-bwa.sourceforge.net\nDownload and install SAMtools (\u003e0.1.17): http://samtools.sourceforge.net/\nDownload and install bedtools (\u003e2.15): http://code.google.com/p/bedtools/\nDownload and install BLAT binaries: http://genome-test.cse.ucsc.edu/~kent/exe/\nDownload and install seqtk: https://github.com/lh3/seqtk\nBe sure that all of these programs are included in your PATH.\n\n### RUNNING ERIC\n\nOnce you have downloaded EricScript, extract the package\n\ntar -xjf ericscript.tar.bz2\n\nMake a copy of the program folder to your favorite location. Before running for the first time EricScript, you need to make ericscript.pl executable:\n\nchmod +x /PATH/TO/ERIC/ericscript.pl\n\nTo get information about running EricScript, digit:\n\n/PATH/TO/ERIC/ericscript.pl --help\n\nIn order to perform chimeric transcript detection, you need to download and build the Ensembl Database of a genome. To list the available genomes, digit:\n\n/PATH/TO/ERIC/ericscript.pl --printdb\n\nAfter a reference id is selected, you need to download and build the corresponding Ensembl Database. In the example below, it's shown how to prepare the database for saccharomyces cerevisiae.\n\n/PATH/TO/ERIC/ericscript.pl --downdb --refid saccharomyces_cerevisiae -db /PATH/TO/YOUR/DBFOLDER\n\nYou can also select a specific ensembl release (\u003e= 70) to download \n\n/PATH/TO/ERIC/ericscript.pl --downdb --refid saccharomyces_cerevisiae -db /PATH/TO/YOUR/DBFOLDER --ensversion 74\n\nTo run EricScript with default parameters (if parameter \"refid\" is not specified the analysis takes the homo sapiens species as default):\n\n/PATH/TO/ERIC/ericscript.pl -db /PATH/TO/YOUR/DBFOLDER --refid saccharomyces_cerevisiae -name SAMPLENAME -o /PATH/TO/OUTPUT/ YOUR_FASTQ_1 YOUR_FASTQ_2 \n\nYou can check if your database is up-to-date by the following:\n\n/PATH/TO/ERIC/ericscript.pl --checkdb\n\n### OUTPUT FILES\n\nThe /PATH/TO/OUTPUT/ folder contains the results of the analysis. Predicted gene fusion products are reported in 2 files:\nsamplename.results.total.csv: contains all the predicted gene fusions.\nsamplename.results.filtered.csv: contains the predicted gene fusions with EricScore \u003e 0.50.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fericscript","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fericscript","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fericscript/lists"}