robertsmac:bismark_v0.6.4 sr320$ echo $PATH

# output# /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/git/bin


export PATH=/Volumes/Bay3/Software/bowtie:${PATH}


-------

Final Alignment report
======================
Sequences analysed in total:     139728554
Number of alignments with a unique best hit from the different alignments:     46463
Mapping efficiency:     0.0%

Sequences with no alignments under any condition:     139581084
Sequences did not map uniquely:     91544
Sequences which were discarded because genomic sequence could not be extracted:     1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:     23771     ((converted) top strand)
CT/GA:     22692     ((converted) bottom strand)
GA/CT:     0     (complementary to (converted) top strand)
GA/GA:     0     (complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:     9463

Final Cytosine Methylation Report
=================================
Total number of C's analysed:     327062

Total methylated C's in CpG context:     51012
Total methylated C's in CHG context:     905
Total methylated C's in CHH context:     5502

Total C to T conversions in CpG context:     18901
Total C to T conversions in CHG context:     32500
Total C to T conversions in CHH context:     218242

C methylated in CpG context:     73.0%
C methylated in CHG context:     2.7%
C methylated in CHH context:     2.5%



Processed 46462 lines from filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam in total
Total number of methylation call strings processed: 46462

Final Cytosine Methylation Report
=================================
Total number of C's analysed:     327062

Total methylated C's in CpG context:     51012
Total methylated C's in CHG context:     905
Total methylated C's in CHH context:     5502

Total C to T conversions in CpG context:     18901
Total C to T conversions in CHG context:     32500
Total C to T conversions in CHH context:     218242

C methylated in CpG context:     73.0%
C methylated in CHG context:     2.7%
C methylated in CHH context:     2.5%


--

ALL FILES

raw reads on bsSeqref.fa

CHG_context_filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam
CHH_context_filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam
CpG_context_filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam
filtered_Unlabeled_NoIndex_L003_R1.fastq_Bismark_mapping_report.txt
filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam