Mercurial > repos > iuc > multiqc

annotate test-data/bismark.txt @ 16:bf675f34b056 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
author iuc
date Sat, 16 May 2020 09:40:45 -0400
parents 3bad335ccea9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
1 Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
2 Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
3 Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
4
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
5 Final Alignment report
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
6 ======================
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
7 Sequences analysed in total: 316390
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
8 Number of alignments with a unique best hit from the different alignments: 220558
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
9 Mapping efficiency: 69.7%
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
10 Sequences with no alignments under any condition: 93928
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
11 Sequences did not map uniquely: 1904
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
12 Sequences which were discarded because genomic sequence could not be extracted: 0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
13
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
14 Number of sequences with unique best (first) alignment came from the bowtie output:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
15 CT/CT: 108352 ((converted) top strand)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
16 CT/GA: 112206 ((converted) bottom strand)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
17 GA/CT: 0 (complementary to (converted) top strand)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
18 GA/GA: 0 (complementary to (converted) bottom strand)
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
19
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
20 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
21
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
22 Final Cytosine Methylation Report
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
23 =================================
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
24 Total number of C's analysed: 5291918
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
25
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
26 Total methylated C's in CpG context: 465068
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
27 Total methylated C's in CHG context: 1358074
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
28 Total methylated C's in CHH context: 3449120
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
29 Total methylated C's in Unknown context: 1499
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
30
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
31 Total unmethylated C's in CpG context: 6399
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
32 Total unmethylated C's in CHG context: 2988
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
33 Total unmethylated C's in CHH context: 10269
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
34 Total unmethylated C's in Unknown context: 454
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
35
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
36 C methylated in CpG context: 98.6%
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
37 C methylated in CHG context: 99.8%
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
38 C methylated in CHH context: 99.7%
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
39 C methylated in Unknown context (CN or CHN): 76.8%