test-datasets lncpipe

nf-core is a collection of high quality Nextflow pipelines.

Content of this repository

NOTE: A full packaged test data set can be downloaded from http://cancerbio.info/pub/lncpipe/testdata.tar.gz

This branch contains test data instruction for the nf-core/lncpipe pipeline.

Run test data of lncpipe

As lncpipe involved integrated analysis of multi samples, we provided a four-sample packaged test data that have two different experiment conditions. To run the test of lncpipe, plz type the following command step by step :

      #prepare test data 
      wget http://cancerbio.info/pub/lncpipe/testdata.tar.gz
      tar -xvzf testdata.tar.gz 
      cd testdata
      # pull the dev branch of lncpipe 
       git clone -b dev https://github.com/nf-core/lncpipe.git
      
      #run test command 
      nextflow run lncpipe -profile test,docker

Test data content

      ├── design.file
      ├── Fastq
      │   ├── dPDLSCs1_1.fastq.gz
      │   ├── dPDLSCs1_2.fastq.gz
      │   ├── dPDLSCs2_1.fastq.gz
      │   ├── dPDLSCs2_2.fastq.gz
      │   ├── uPDLSCs1_1.fastq.gz
      │   ├── uPDLSCs1_2.fastq.gz
      │   ├── uPDLSCs2_1.fastq.gz
      │   └── uPDLSCs2_2.fastq.gz
      └── Genome
          ├── chr22.fa
          ├── gencode.chr22.gtf
          ├── hisat_index
          │   ├── chr22.1.ht2
          │   ├── chr22.2.ht2
          │   ├── chr22.3.ht2
          │   ├── chr22.4.ht2
          │   ├── chr22.5.ht2
          │   ├── chr22.6.ht2
          │   ├── chr22.7.ht2
          │   └── chr22.8.ht2
          └── lncipedia.chr22.gtf

• design.file store the exprimental design for performing comparision

      D:dPDLSCs1,dPDLSCs2
      u:uPDLSCs1,uPDLSCs2

• Fastq folder contains paired, compressed fastq files, also known as raw reads.

• Genome folder contains several files explained below:

  • chr22.fa genome reference of chromosome 22 with fasta format.

  • hisat_index folder contains the hisat2 index file build from chr22.fa

  • lncipedia.chr22.gtf GTF files grepped from lncpedia_4.0.gtf

  • gencode.chr22.gtf GTP files grepped from GENCODE