view test-data/bismark_data.txt @ 15:d6579f50e622 draft

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Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0)
Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)
Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet

Final Alignment report
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Sequences analysed in total:	316390
Number of alignments with a unique best hit from the different alignments:	220558
Mapping efficiency:	69.7%
Sequences with no alignments under any condition:	93928
Sequences did not map uniquely:	1904
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	108352	((converted) top strand)
CT/GA:	112206	((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:	0

Final Cytosine Methylation Report
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Total number of C's analysed:	5291918

Total methylated C's in CpG context:	465068
Total methylated C's in CHG context:	1358074
Total methylated C's in CHH context:	3449120
Total methylated C's in Unknown context:	1499

Total unmethylated C's in CpG context:	6399
Total unmethylated C's in CHG context:	2988
Total unmethylated C's in CHH context:	10269
Total unmethylated C's in Unknown context:	454

C methylated in CpG context:	98.6%
C methylated in CHG context:	99.8%
C methylated in CHH context:	99.7%
C methylated in Unknown context (CN or CHN):	76.8%