LncPipeTestData

This repo contains a test case for running LncPipe.
Testdata can be download here

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