comparison test-data/bismark_data.txt @ 0:8f25feb85166 draft

planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
author engineson
date Fri, 27 May 2016 06:22:43 -0400
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-1:000000000000 0:8f25feb85166
1 Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0)
2 Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)
3 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
4
5 Final Alignment report
6 ======================
7 Sequences analysed in total: 316390
8 Number of alignments with a unique best hit from the different alignments: 220558
9 Mapping efficiency: 69.7%
10 Sequences with no alignments under any condition: 93928
11 Sequences did not map uniquely: 1904
12 Sequences which were discarded because genomic sequence could not be extracted: 0
13
14 Number of sequences with unique best (first) alignment came from the bowtie output:
15 CT/CT: 108352 ((converted) top strand)
16 CT/GA: 112206 ((converted) bottom strand)
17 GA/CT: 0 (complementary to (converted) top strand)
18 GA/GA: 0 (complementary to (converted) bottom strand)
19
20 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
21
22 Final Cytosine Methylation Report
23 =================================
24 Total number of C's analysed: 5291918
25
26 Total methylated C's in CpG context: 465068
27 Total methylated C's in CHG context: 1358074
28 Total methylated C's in CHH context: 3449120
29 Total methylated C's in Unknown context: 1499
30
31 Total unmethylated C's in CpG context: 6399
32 Total unmethylated C's in CHG context: 2988
33 Total unmethylated C's in CHH context: 10269
34 Total unmethylated C's in Unknown context: 454
35
36 C methylated in CpG context: 98.6%
37 C methylated in CHG context: 99.8%
38 C methylated in CHH context: 99.7%
39 C methylated in Unknown context (CN or CHN): 76.8%