http://www.ncbi.nlm.nih.gov/genome?term=lambda%20phage

phage_lambda_genome.fasta




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bsmap



./bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/filtered_174gm_A_ACTGATA_L002_R1.fastq -d /Volumes/web/cnidarian/phage_lambda_genome.fasta -o /Volumes/web/cnidarian/BSMAP_Gonad_QC_lambda.sam -p 2

Total number of aligned reads: 2853 (0.17%)

output
http://eagle.fish.washington.edu/cnidarian/BSMAP_Gonad_QC_lambda.sam




./bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/filtered_174gm_A_ACTGATA_L002_R1.fastq -d /Volumes/web/cnidarian/phage_lambda_genome.fasta -o /Volumes/web/cnidarian/BSMAP_Gonad_QC_lambda_B.sam -p 2 -n 1

Total number of aligned reads: 2854 (0.17%)

output
http://eagle.fish.washington.edu/cnidarian/BSMAP_Gonad_QC_lambda_B.sam



methratio 

python methratio.py -d /Volumes/web/cnidarian/phage_lambda_genome.fasta -u -z -o /Volumes/web/cnidarian/OUTzu_methratioBSMAP_gonadQC_lambda_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/web/cnidarian/BSMAP_Gonad_QC_lambda_B.sam

output:
http://eagle.fish.washington.edu/cnidarian/OUTzu_methratioBSMAP_gonadQC_lambda_A.txt


15k lines