Be sure to follow instruction in readme file

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./bsmap -a /Volumes/Bay4\ scratch/temp/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -d  /Volumes/NGS\ Drive/Oyster\ Genome/oyster.v9_M.fa -o /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam -p 2

Input reference file: /Volumes/NGS Drive/Oyster Genome/oyster.v9_M.fa      (format: FASTA)

Load in 60 db seqs, total size 77580364 bp. 2 secs passed

total_kmers: 43046721

Create seed table. 11 secs pbsmapassed

max number of mismatches: read_length * 8%      max gap size: 0

kmer cut-off ratio:5e-07

max multi-hits: 100     max Ns: 5     seed size: 16     index interval: 4

quality cutoff: 0     base quality char: '!'

min fragment size:28     max fragemt size:500

start from read #1     end at read #4294967295

additional alignment: T in reads => C in reference

mapping strand: ++,-+

Single-end alignment(2 threads)

Input read file: /Volumes/Bay4 scratch/temp/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq      (format: FASTQ)

Output file: /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam      (format: SAM)

Thread #1:      50000 reads finished. 12 secs passed

Thread #0:      100000 reads finished. 12 secs passed

Thread #1:      150000 reads finished. 13 secs passed

OUTPUT: http://aquacul4.fish.washington.edu/~steven/armina/BSMAP_output_trimmed_v9_M.sam

Description

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methratio

python methratio.py -d /Volumes/NGS\ Drive/Oyster\ Genome/oyster.v9_M.fa -z -o /Volumes/AquaculX/armina/OUTz_methratioBSMAP_v9_M_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam 

@ Wed Sep 19 15:06:29 2012: writing /Volumes/AquaculX/armina/OUTz_methratioBSMAP_v9_M_A.txt ...

python methratio.py -d /Volumes/NGS\ Drive/Oyster\ Genome/oyster.v9_M.fa -z -u -o /Volumes/AquaculX/armina/OUTzu_methratioBSMAP_v9_M_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam 

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What is next?