change output to BSMAP folder
./bsmap -a /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -d cgigas_alpha_v032.fa -o BSMAP_output_trimmed_v0_3_2_A.sam -p 4
BSMAP v2.42
Start at: Tue Mar 13 11:40:52 2012
Load in 272 db seqs, total size 12727625 bp. 0 secs passed
total_kmers: 43046721
Create seed table. 3 secs passed
max mismatches: 2 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
param.chains:0
mapping strand: ++,-+
Single read alignment(4 threads)
Query: /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq Reference: cgigas_alpha_v032.fa Output: BSMAP_output_trimmed_v0_3_2_A.sam
139600000 reads finished. 966 secs passed
139650000 reads finished. 966 secs passed
Total number of aligned reads: 18998442 (14%)
Done.
Finished at Tue Mar 13 11:56:58 2012
Total time consumed: 966 secs
OUTPUT
http://aquacul4.fish.washington.edu/~steven/ballyhoo/BSMAP_output_trimmed_v0_3_2_A.sam
--
methratio
python methratio.py -d cgigas_alpha_v032.fa -z -o OUTz_methratioBSMAP_v032_A.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_2_A.sam
OUTPUT
-
python methratio.py -d cgigas_alpha_v032.fa -z -u -o OUTzu_methratioBSMAP_v032_A.txt -s /Volumes/Bay3/Software/samtools BSMAP_output_trimmed_v0_3_2_A.sam
OUTPUT