Mercurial > repos > bgruening > bismark

comparison test-data/mapping_report_mate.txt @ 14:b6aa3b6ba129 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
author bgruening
date Tue, 30 Jul 2019 10:33:02 -0400
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13:f211753166bd 14:b6aa3b6ba129
1 Bismark report for: input1_fq_1.fq and input1_fq_2.fq (version: v0.22.1)
2 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpAHSx4i/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 0 --maxins 500 --quiet
3 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
4
5 Final Alignment report
6 ======================
7 Sequence pairs analysed in total: 1000
8 Number of paired-end alignments with a unique best hit: 0
9 Mapping efficiency: 0.0%
10 Sequence pairs with no alignments under any condition: 1000
11 Sequence pairs did not map uniquely: 0
12 Sequence pairs which were discarded because genomic sequence could not be extracted: 0
13
14 Number of sequence pairs with unique best (first) alignment came from the bowtie output:
15 CT/GA/CT: 0 ((converted) top strand)
16 GA/CT/CT: 0 (complementary to (converted) top strand)
17 GA/CT/GA: 0 (complementary to (converted) bottom strand)
18 CT/GA/GA: 0 ((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: 0
25
26 Total methylated C's in CpG context: 0
27 Total methylated C's in CHG context: 0
28 Total methylated C's in CHH context: 0
29 Total methylated C's in Unknown context: 0
30
31 Total unmethylated C's in CpG context: 0
32 Total unmethylated C's in CHG context: 0
33 Total unmethylated C's in CHH context: 0
34 Total unmethylated C's in Unknown context: 0
35
36 Can't determine percentage of methylated Cs in CpG context if value was 0
37 Can't determine percentage of methylated Cs in CHG context if value was 0
38 Can't determine percentage of methylated Cs in CHH context if value was 0
39 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
40
41
42 Bismark completed in 0d 0h 0m 5s