Quick Start

1. Specific the path of references (.fasta) and samples (.fastq) in a configure file (.YAML).

   For example, write down and save the following block into a text file and named it as data.yaml.

   reference:
     genes:
       fa: ./ref/genes.fa
     genome:
       fa: /data/reference/genome/Mus_musculus/GRCm39.fa
       star: /data/reference/genome/Mus_musculus/star/GRCm39.release108
   
   samples:
     mESCWT-rep1-input:
       data:
         - R1: ./test/IP16.fastq.gz
       group: mESCWT
       treated: false
     mESCWT-rep1-treated:
       data:
         - R1: ./test/IP4.fastq.gz
       group: mESCWT
       treated: true
     mESCWT-rep2-treated:
       data:
         - R1: ./test/IP5.fastq.gz
       group: mESCWT
       treated: true
   

2. Run all the analysis by one command:

   snakemake -s Snakefile -c config.yaml