Mercurial > repos > bgruening > bismark

comparison test-data/mapping_report.txt @ 8:9bfe38410155 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author bgruening
date Wed, 22 Aug 2018 08:09:42 -0400
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children f211753166bd
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7:fcadce4d9a06 8:9bfe38410155
1 Bismark report for: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat (version: v0.20.0)
2 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
3 Bismark was run with Bowtie 2 against the bisulfite genome of /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ 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: 44115
8 Number of alignments with a unique best hit from the different alignments: 554
9 Mapping efficiency: 1.3%
10 Sequences with no alignments under any condition: 43115
11 Sequences did not map uniquely: 446
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: 230 ((converted) top strand)
16 CT/GA: 324 ((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: 8563
25
26 Total methylated C's in CpG context: 245
27 Total methylated C's in CHG context: 51
28 Total methylated C's in CHH context: 114
29 Total methylated C's in Unknown context: 1
30
31 Total unmethylated C's in CpG context: 133
32 Total unmethylated C's in CHG context: 1762
33 Total unmethylated C's in CHH context: 6258
34 Total unmethylated C's in Unknown context: 5
35
36 C methylated in CpG context: 64.8%
37 C methylated in CHG context: 2.8%
38 C methylated in CHH context: 1.8%
39 C methylated in Unknown context (CN or CHN): 16.7%
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42 Bismark completed in 0d 0h 0m 8s