comparison test-data/mapping_report_short.txt @ 13:f211753166bd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
author bgruening
date Tue, 30 Jul 2019 06:30:36 -0400
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12:78c791a11b4c 13:f211753166bd
1 Bismark report for: input_1.fq (version: v0.22.1)
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 /tmp/tmpVM2AEy/ 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: 1000
8 Number of alignments with a unique best hit from the different alignments: 8
9 Mapping efficiency: 0.8%
10 Sequences with no alignments under any condition: 983
11 Sequences did not map uniquely: 9
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: 6 ((converted) top strand)
16 CT/GA: 2 ((converted) bottom strand)
17 GA/CT: 0 (complementary to (converted) top strand)
18 GA/GA: 0 (complementary to (converted) bottom strand)
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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: 143
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26 Total methylated C's in CpG context: 3
27 Total methylated C's in CHG context: 2
28 Total methylated C's in CHH context: 3
29 Total methylated C's in Unknown context: 0
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31 Total unmethylated C's in CpG context: 1
32 Total unmethylated C's in CHG context: 36
33 Total unmethylated C's in CHH context: 98
34 Total unmethylated C's in Unknown context: 0
35
36 C methylated in CpG context: 75.0%
37 C methylated in CHG context: 5.3%
38 C methylated in CHH context: 3.0%
39 Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0
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42 Bismark completed in 0d 0h 0m 5s