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.

   genome_index: ~/reference/genome/Homo_sapiens/hisat2_tx_3n/GRCh38.release110
   
   reference:
     contamination:
       - test/ref/contamination.fa.gz
     genes:
       - test/ref/spikein.fa
       - test/ref/human_rRNA.fa
   
   samples:
     HeLa-treat-rep1:
       data:
         - R1: test/data/SRR21070405_1.fastq.gz
           R2: test/data/SRR21070405_2.fastq.gz
         - R1: test/data/SRR21070406_1.fastq.gz
     HeLa-treat-rep2:
       data:
         - R1: test/data/SRR21070404_1.fastq.gz
   

2. Run all the analysis by one command:

   git clone --recurse-submodules https://github.com/y9c/m6A-eTAMseq.git
   snakemake -s Snakefile -c config.yaml