example on SE
./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
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:
--
./bsmap -a /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/cnidarian/phage_lambda_genome.fasta -o /Volumes/web/cnidarian/BSMAP_output_PE_lambda_A.sam -p 8
python
methratio.py -d /Volumes/web/cnidarian/phage_lambda_genome.fasta -u -z -o /Volumes/web/cnidarian/OUTzu_methratioBSMAP_gonadPE_lambda_A.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Volumes/web/cnidarian/BSMAP_output_PE_lambda_A.sam
total 394092 valid mappings, 24180 covered cytosines, average coverage: 237.75 fold.