Quick start with test data

Before running circPipe, users should check if all the required tools and databases are available on the system(that is, either on the local machine or on the HPC facility).circPipe accepts raw reads, annotations and genome reference as input to process the whole pipeline. At present, we mainly focus on human genome.

Here, we will show the usage of circPipe step by step using our test data in a linux system as an example.

Step 1. Download test data

wegt http://cancerbio.info/pub/circpipe/testdata.tar.gz
tar -xvzf testdata.tar.gz
cd testdata

Step 2. Install NextFlow

curl -fsSL get.nextflow.io | bash
mv nextflow ~/bin/

Step 3. Get the lastest circPipe

mkdir -p ~/my-pipelines/
git clone https://github.com/likelet/circPipe.git
cd ~/my_data/
nextflow run ~/my-pipelines/circPipe

Step 4. Pipeline configuration

By default, circPipe runs with the standard configuration profile conf/base.config under the github.

Step 3. Run the analysis command

#(Make sure all the config files have got ready as our pipeline demand)
 nextflow -c nextflow.config main.nf

Result content(expected result)

Note

After finishing running the pipeline, users will get final results, details of which are described in the part of output section