Mercurial > repos > bgruening > bismark
comparison test-data/mapping_report_mate_two_samples.txt @ 21:120b7b35e442 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author | bgruening |
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date | Thu, 22 Apr 2021 17:05:46 +0000 |
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20:ff6ee551b153 | 21:120b7b35e442 |
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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/tmp8oj0_k8v/ 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 7s | |
43 Bismark report for: input2.fq_1.fq and input2.fq_2.fq (version: v0.22.1) | |
44 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmp8oj0_k8v/ 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 | |
45 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) | |
46 | |
47 Final Alignment report | |
48 ====================== | |
49 Sequence pairs analysed in total: 1000 | |
50 Number of paired-end alignments with a unique best hit: 0 | |
51 Mapping efficiency: 0.0% | |
52 Sequence pairs with no alignments under any condition: 1000 | |
53 Sequence pairs did not map uniquely: 0 | |
54 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 | |
55 | |
56 Number of sequence pairs with unique best (first) alignment came from the bowtie output: | |
57 CT/GA/CT: 0 ((converted) top strand) | |
58 GA/CT/CT: 0 (complementary to (converted) top strand) | |
59 GA/CT/GA: 0 (complementary to (converted) bottom strand) | |
60 CT/GA/GA: 0 ((converted) bottom strand) | |
61 | |
62 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 | |
63 | |
64 Final Cytosine Methylation Report | |
65 ================================= | |
66 Total number of C's analysed: 0 | |
67 | |
68 Total methylated C's in CpG context: 0 | |
69 Total methylated C's in CHG context: 0 | |
70 Total methylated C's in CHH context: 0 | |
71 Total methylated C's in Unknown context: 0 | |
72 | |
73 Total unmethylated C's in CpG context: 0 | |
74 Total unmethylated C's in CHG context: 0 | |
75 Total unmethylated C's in CHH context: 0 | |
76 Total unmethylated C's in Unknown context: 0 | |
77 | |
78 Can't determine percentage of methylated Cs in CpG context if value was 0 | |
79 Can't determine percentage of methylated Cs in CHG context if value was 0 | |
80 Can't determine percentage of methylated Cs in CHH context if value was 0 | |
81 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 | |
82 | |
83 | |
84 Bismark completed in 0d 0h 0m 9s |