Mercurial > repos > bgruening > bismark

comparison test-data/mapping_report_pbat.txt @ 17:aa9bf0f29a9f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
author bgruening
date Wed, 28 Aug 2019 07:08:45 -0400
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16:a4504327c890 17:aa9bf0f29a9f
1 Bismark report for: input_1.fq (version: v0.22.1)
2 Option '--pbat' specified: alignments to original strands (OT and OB) strands were ignored (i.e. not performed)
3 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpuqE7r1/ 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: 13
9 Mapping efficiency: 0.0%
10 Sequences with no alignments under any condition: 44059
11 Sequences did not map uniquely: 43
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: 0 ((converted) top strand)
16 CT/GA: 0 ((converted) bottom strand)
17 GA/CT: 11 (complementary to (converted) top strand)
18 GA/GA: 2 (complementary to (converted) bottom strand)
19
20 Final Cytosine Methylation Report
21 =================================
22 Total number of C's analysed: 307
23
24 Total methylated C's in CpG context: 1
25 Total methylated C's in CHG context: 3
26 Total methylated C's in CHH context: 227
27 Total methylated C's in Unknown context: 0
28
29 Total unmethylated C's in CpG context: 1
30 Total unmethylated C's in CHG context: 4
31 Total unmethylated C's in CHH context: 71
32 Total unmethylated C's in Unknown context: 0
33
34 C methylated in CpG context: 50.0%
35 C methylated in CHG context: 42.9%
36 C methylated in CHH context: 76.2%
37 Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0
38
39
40 Bismark completed in 0d 0h 0m 7s