Mercurial > repos > iuc > multiqc
comparison test-data/bismark.txt @ 0:3bad335ccea9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
| author | iuc |
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| date | Tue, 24 Oct 2017 06:29:59 -0400 |
| parents | |
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| -1:000000000000 | 0:3bad335ccea9 |
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| 1 Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0) | |
| 2 Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!) | |
| 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 | |
| 4 | |
| 5 Final Alignment report | |
| 6 ====================== | |
| 7 Sequences analysed in total: 316390 | |
| 8 Number of alignments with a unique best hit from the different alignments: 220558 | |
| 9 Mapping efficiency: 69.7% | |
| 10 Sequences with no alignments under any condition: 93928 | |
| 11 Sequences did not map uniquely: 1904 | |
| 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: 108352 ((converted) top strand) | |
| 16 CT/GA: 112206 ((converted) bottom strand) | |
| 17 GA/CT: 0 (complementary to (converted) top strand) | |
| 18 GA/GA: 0 (complementary to (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: 5291918 | |
| 25 | |
| 26 Total methylated C's in CpG context: 465068 | |
| 27 Total methylated C's in CHG context: 1358074 | |
| 28 Total methylated C's in CHH context: 3449120 | |
| 29 Total methylated C's in Unknown context: 1499 | |
| 30 | |
| 31 Total unmethylated C's in CpG context: 6399 | |
| 32 Total unmethylated C's in CHG context: 2988 | |
| 33 Total unmethylated C's in CHH context: 10269 | |
| 34 Total unmethylated C's in Unknown context: 454 | |
| 35 | |
| 36 C methylated in CpG context: 98.6% | |
| 37 C methylated in CHG context: 99.8% | |
| 38 C methylated in CHH context: 99.7% | |
| 39 C methylated in Unknown context (CN or CHN): 76.8% |