Mercurial > repos > bgruening > bismark
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 |
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| date | Tue, 30 Jul 2019 06:30:36 -0400 |
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| 12:78c791a11b4c | 13:f211753166bd |
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| 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) | |
| 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: 143 | |
| 25 | |
| 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 | |
| 30 | |
| 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 | |
| 40 | |
| 41 | |
| 42 Bismark completed in 0d 0h 0m 5s |