Tutorial

1. Download the sample input file

$ curl -O http://paoyang.ipmb.sinica.edu.tw/public_data/methgo_demo.tar.gz
$ tar xvfz methgo_demo.tar.gz
$ cd methgo_demo/data

2. Run COV module:

$ methgo cov genome.fa demo.CGmap

3. Run MET module:

$ methgo met genes.gtf genome.fa demo.CGmap

4. Run TXN module:

$ methgo txn -t methgo/scripts/txn/tair10_txn -l ATHB1_binding_site_motif,CCA1_binding_site_motif -c demo.CGmap

5. Run SNP module:

$ methgo snp -g genome.fa demo.sorted.bam

6. Run CNV module:

$ methgo cnv genome.fa.fai demo.sorted.bam