TJGR BSMAP new data (QC)

./bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/filtered_174gm_A_ACTGATA_L002_R1.fastq -d /Volumes/NGS\ Drive/Oyster\ Genome/genome_v9/oyster.v9.fa -o /Volumes/web/cnidarian/BSMAP_Gonad_QC_oyster_v9.sam -p 2

(entire genome)

Total number of aligned reads: 1270581 (74%)

Output:

http://eagle.fish.washington.edu/cnidarian/BSMAP_Gonad_QC_oyster_v9.sam

methratio

python methratio.py -d /Volumes/NGS\ Drive/Oyster\ Genome/genome_v9/oyster.v9.fa -u -o /Volumes/web/cnidarian/OUTu_methratioBSMAP_gondadQC_v9_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/web/cnidarian/BSMAP_Gonad_QC_oyster_v9.sam

Output:

http://eagle.fish.washington.edu/cnidarian/OUTu_methratioBSMAP_gondadQC_v9_A.txt

73 on positive strand have 4x coverage. -methylation present (unconverted cystosine_

python methratio.py -d /Volumes/NGS\ Drive/Oyster\ Genome/genome_v9/oyster.v9.fa -u -q -z -o /Volumes/web/cnidarian/OUTzu_methratioBSMAP_gondadQC_v9_B.txt -s /Volumes/Bay3/Software/samtools /Volumes/web/cnidarian/BSMAP_Gonad_QC_oyster_v9.sam

output

http://eagle.fish.washington.edu/cnidarian/OUTzu_methratioBSMAP_gondadQC_v9_B.txt

./bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Oyster_gonad_Bisulfite/filtered_174gm_A_ACTGATA_L002_R1.fastq -d /Volumes/web/cnidarian/oyster.v9_90.fa -o /Volumes/web/cnidarian/BSMAP_Gonad_QC_oyster_v9_90.sam -p 2