./bsmap -a /Volumes/web/cnidarian/filtered_Unlabeled_NoIndex_L003_R1.fastq.gz -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -o /Volumes/web/cnidarian/BSMAP_output_gillMBD_v9_90.sam

Total number of aligned reads: 116535031 (83%)

python methratio.py -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -u -z -o /Volumes/web/cnidarian/OUT_methratio_gillMBD_v9_90_B.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Volumes/web/cnidarian/BSMAP_output_gillMBD_v9_90.sam

total 73925205 valid mappings, 90744317 covered cytosines, average coverage: 4.75 fold.

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http://eagle.fish.washington.edu/cnidarian/TJGR_GillMBD_mCpG_10xcov.bed