Mercurial > repos > bgruening > bismark
comparison test-data/mapping_report_mate.txt @ 14:b6aa3b6ba129 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
| author | bgruening |
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| date | Tue, 30 Jul 2019 10:33:02 -0400 |
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| 13:f211753166bd | 14:b6aa3b6ba129 |
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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/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 |