Mercurial > repos > bgruening > bismark
diff 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 |
|---|---|
| date | Tue, 30 Jul 2019 06:30:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_report_short.txt Tue Jul 30 06:30:36 2019 -0400 @@ -0,0 +1,42 @@ +Bismark report for: input_1.fq (version: v0.22.1) +Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) +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 + +Final Alignment report +====================== +Sequences analysed in total: 1000 +Number of alignments with a unique best hit from the different alignments: 8 +Mapping efficiency: 0.8% +Sequences with no alignments under any condition: 983 +Sequences did not map uniquely: 9 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 6 ((converted) top strand) +CT/GA: 2 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 143 + +Total methylated C's in CpG context: 3 +Total methylated C's in CHG context: 2 +Total methylated C's in CHH context: 3 +Total methylated C's in Unknown context: 0 + +Total unmethylated C's in CpG context: 1 +Total unmethylated C's in CHG context: 36 +Total unmethylated C's in CHH context: 98 +Total unmethylated C's in Unknown context: 0 + +C methylated in CpG context: 75.0% +C methylated in CHG context: 5.3% +C methylated in CHH context: 3.0% +Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 + + +Bismark completed in 0d 0h 0m 5s