! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap -a /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_174gm_A_NoIndex_L006_R1.fastq -b /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_174gm_A_NoIndex_L006_R2.fastq -d /Volumes/web/cnidarian/Cgigas_mito_genome.fasta -o /Volumes/web/cnidarian/BiGo_mito.sam -p 3

!python /Volumes/Bay3/Software/BSMAP/bsmap-2.74/methratio.py -d /Volumes/web/cnidarian/Cgigas_mito_genome.fasta -u -z -g -o  /Volumes/web/cnidarian/BiGo_mito_methratio_A.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools /Volumes/web/cnidarian/BiGo_mito.sam

!head /Volumes/web/cnidarian/BiGo_mito_methratio_A.txt

!fgrep -c "C" /Volumes/web/cnidarian/Cgigas_mito_genome.fasta

!head /Volumes/web/cnidarian/Cgigas_mito_genome.fasta