https://github.com/likelet/lncpipetestdata
A test data repo for LncPipe
https://github.com/likelet/lncpipetestdata
Last synced: 11 months ago
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A test data repo for LncPipe
- Host: GitHub
- URL: https://github.com/likelet/lncpipetestdata
- Owner: likelet
- Created: 2018-10-09T06:47:03.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2021-11-19T01:54:35.000Z (about 4 years ago)
- Last Synced: 2025-01-07T20:45:54.492Z (12 months ago)
- Language: HTML
- Size: 1.07 MB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# LncPipeTestData
This repo contains a test case for running LncPipe.
Testdata can be download [here](http://download.omicsbio.info/files/DAtools/testdata.tar.gz)
## Data Information
Only a subset of the whole dataset (trimmed for chrX only) were put on this repo for improving testing efficiency for LncPipe.
The file includes
* Fastq files with properly named `Fastq/*.gz`
* Genome reference from GENCODE `Genome/chrX.fa`
* Hisat2 index of the genome reference `Genome/hisat2Index*.ht2`, generated by following command
hisat2-build chrX.fa chrX
* GENCODE ANNOTATION file `Genome/gencode.v25.annotation.chrX.gtf`
* LncPipedia ANNOTATION file `Genome/lncipedia_4_0.chrX.gtf`
* Experimental design file `design.file`
* 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)
## Test command (Assume that docker and nextflow were properly preinstalled )
* __Step 1__. Download the test data
wget http://download.omicsbio.info/files/DAtools/testdata.tar.gz
tar -xvzf LncPipeTestData.tar.gz
cd LncPipeTestData
* __Step 2__. Get the lastest lncPipe
git clone https://github.com/likelet/LncPipe.git
* __Step 3__. Run the analysis command (about 10 mins)
#(run the this `cmd` if your are using a centos 7.0 linux system , this cmd can temperally set the selinux into permissive mode )
sudo setenforce 0
nextflow run LncPipe/LncRNAanalysisPipe.nf -profile docker,test -with-trace -resume -with-timeline timeline.html
## Result content (expected result)
```
├── hisat_alignment
│ ├── R1126N.hisat2_summary.txt
│ ├── R1126N.sort.bam
│ ├── R1126T.hisat2_summary.txt
│ ├── R1126T.sort.bam
│ ├── R1130N.hisat2_summary.txt
│ ├── R1130N.sort.bam
│ ├── R1130T.hisat2_summary.txt
│ ├── R1130T.sort.bam
│ ├── R1134N.hisat2_summary.txt
│ ├── R1134N.sort.bam
│ ├── R1134T.hisat2_summary.txt
│ ├── R1134T.sort.bam
│ ├── S483N.hisat2_summary.txt
│ ├── S483N.sort.bam
│ ├── S483T.hisat2_summary.txt
│ ├── S483T.sort.bam
│ ├── S502N.hisat2_summary.txt
│ ├── S502N.sort.bam
│ ├── S502T.hisat2_summary.txt
│ └── S502T.sort.bam
├── Identified_lncRNA
│ ├── all_lncRNA_for_classifier.gtf
│ ├── final_all.fa
│ ├── final_all.gtf
│ ├── lncRNA_classification.txt
│ ├── lncRNA.fa
│ ├── protein_coding.fa
│ └── protein_coding.final.gtf
├── LncPipeReports
│ ├── figures
│ ├── libs
│ ├── reporter_files
│ ├── reporter.html
│ └── tables
├── Merged_assemblies
│ └── merged.gtf
├── QC
│ ├── R1126N_fastp.html
│ ├── R1126T_fastp.html
│ ├── R1130N_fastp.html
│ ├── R1130T_fastp.html
│ ├── R1134N_fastp.html
│ ├── R1134T_fastp.html
│ ├── S483N_fastp.html
│ ├── S483T_fastp.html
│ ├── S502N_fastp.html
│ └── S502T_fastp.html
└── Quantification
├── kallisto.count.txt
└── kallisto.tpm.txt
```
## Run information
## another test repo for `lncpipe `
https://github.com/nf-core/test-datasets/blob/lncpipe/README.md