{"id":19434410,"url":"https://github.com/likelet/lncpipetestdata","last_synced_at":"2026-02-07T03:31:07.094Z","repository":{"id":86652039,"uuid":"152201314","full_name":"likelet/LncPipeTestData","owner":"likelet","description":"A test data repo for LncPipe","archived":false,"fork":false,"pushed_at":"2021-11-19T01:54:35.000Z","size":1121,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-26T13:38:34.901Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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":"2018-10-09T06:47:03.000Z","updated_at":"2021-11-19T01:54:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"74535483-898c-4cfc-89d3-a26ed1429a1f","html_url":"https://github.com/likelet/LncPipeTestData","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/likelet/LncPipeTestData","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLncPipeTestData","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLncPipeTestData/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLncPipeTestData/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLncPipeTestData/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/likelet","download_url":"https://codeload.github.com/likelet/LncPipeTestData/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FLncPipeTestData/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29185344,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-07T00:44:15.062Z","status":"online","status_checked_at":"2026-02-07T02:00:07.217Z","response_time":63,"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":[],"created_at":"2024-11-10T14:46:21.423Z","updated_at":"2026-02-07T03:31:07.070Z","avatar_url":"https://github.com/likelet.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# LncPipeTestData\n\nThis repo contains a test case for running LncPipe.  \nTestdata can be download [here](http://download.omicsbio.info/files/DAtools/testdata.tar.gz)\n\n## Data Information   \n\nOnly a subset of the whole dataset (trimmed for chrX only) were put on this repo for improving testing efficiency for LncPipe. \nThe file includes  \n\n* Fastq files with properly named `Fastq/*.gz`  \n\n* Genome reference from GENCODE `Genome/chrX.fa` \n\n* Hisat2 index of the genome reference `Genome/hisat2Index*.ht2`, generated by following command  \n\n        hisat2-build chrX.fa chrX  \n    \n* GENCODE ANNOTATION file `Genome/gencode.v25.annotation.chrX.gtf`\n\n* LncPipedia ANNOTATION file `Genome/lncipedia_4_0.chrX.gtf`\n\n* Experimental design file `design.file`\n\n* nextflow running config file `docker.config` (deprecated, now all config file were moved to the `conf` folder, users could configure the parameter their and run LncPipe with a `-profile` parameter)\n\n\n## Test command  (Assume that docker and nextflow were properly preinstalled )\n\n* __Step 1__. Download the test data \n\n        wget http://download.omicsbio.info/files/DAtools/testdata.tar.gz\n        tar -xvzf LncPipeTestData.tar.gz\n        cd LncPipeTestData\n\n* __Step 2__. Get the lastest lncPipe  \n\n        git clone https://github.com/likelet/LncPipe.git \n\n* __Step 3__. Run the analysis command  (about 10 mins)\n\n        #(run the this `cmd` if your are using a centos 7.0 linux system , this cmd can temperally set the selinux into permissive mode )\n        sudo setenforce 0 \n        \n        nextflow run LncPipe/LncRNAanalysisPipe.nf -profile docker,test -with-trace -resume -with-timeline timeline.html\n\n\n## Result content (expected result)\n        ```\n        ├── hisat_alignment\n        │   ├── R1126N.hisat2_summary.txt\n        │   ├── R1126N.sort.bam\n        │   ├── R1126T.hisat2_summary.txt\n        │   ├── R1126T.sort.bam\n        │   ├── R1130N.hisat2_summary.txt\n        │   ├── R1130N.sort.bam\n        │   ├── R1130T.hisat2_summary.txt\n        │   ├── R1130T.sort.bam\n        │   ├── R1134N.hisat2_summary.txt\n        │   ├── R1134N.sort.bam\n        │   ├── R1134T.hisat2_summary.txt\n        │   ├── R1134T.sort.bam\n        │   ├── S483N.hisat2_summary.txt\n        │   ├── S483N.sort.bam\n        │   ├── S483T.hisat2_summary.txt\n        │   ├── S483T.sort.bam\n        │   ├── S502N.hisat2_summary.txt\n        │   ├── S502N.sort.bam\n        │   ├── S502T.hisat2_summary.txt\n        │   └── S502T.sort.bam\n        ├── Identified_lncRNA\n        │   ├── all_lncRNA_for_classifier.gtf\n        │   ├── final_all.fa\n        │   ├── final_all.gtf\n        │   ├── lncRNA_classification.txt\n        │   ├── lncRNA.fa\n        │   ├── protein_coding.fa\n        │   └── protein_coding.final.gtf\n        ├── LncPipeReports\n        │   ├── figures\n        │   ├── libs\n        │   ├── reporter_files\n        │   ├── reporter.html\n        │   └── tables\n        ├── Merged_assemblies\n        │   └── merged.gtf\n        ├── QC\n        │   ├── R1126N_fastp.html\n        │   ├── R1126T_fastp.html\n        │   ├── R1130N_fastp.html\n        │   ├── R1130T_fastp.html\n        │   ├── R1134N_fastp.html\n        │   ├── R1134T_fastp.html\n        │   ├── S483N_fastp.html\n        │   ├── S483T_fastp.html\n        │   ├── S502N_fastp.html\n        │   └── S502T_fastp.html\n        └── Quantification\n            ├── kallisto.count.txt\n            └── kallisto.tpm.txt\n        ```\n## Run information \n\n![timeline](https://github.com/likelet/LncPipeTestData/blob/master/timeplot.png)\n\n\n## another test repo for `lncpipe `\n\nhttps://github.com/nf-core/test-datasets/blob/lncpipe/README.md \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Flncpipetestdata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Flncpipetestdata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Flncpipetestdata/lists"}