Mercurial > repos > bgruening > bismark
diff test-data/mapping_report_custom.txt @ 16:a4504327c890 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
| author | bgruening |
|---|---|
| date | Wed, 21 Aug 2019 12:59:48 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_report_custom.txt Wed Aug 21 12:59:48 2019 -0400 @@ -0,0 +1,42 @@ +Bismark report for: input_1.fq.gz (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/tmp53fiEn/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.8 --ignore-quals --quiet + +Final Alignment report +====================== +Sequences analysed in total: 44115 +Number of alignments with a unique best hit from the different alignments: 1992 +Mapping efficiency: 4.5% +Sequences with no alignments under any condition: 40786 +Sequences did not map uniquely: 1337 +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: 832 ((converted) top strand) +CT/GA: 1160 ((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: 31956 + +Total methylated C's in CpG context: 564 +Total methylated C's in CHG context: 249 +Total methylated C's in CHH context: 882 +Total methylated C's in Unknown context: 36 + +Total unmethylated C's in CpG context: 608 +Total unmethylated C's in CHG context: 6183 +Total unmethylated C's in CHH context: 23470 +Total unmethylated C's in Unknown context: 232 + +C methylated in CpG context: 48.1% +C methylated in CHG context: 3.9% +C methylated in CHH context: 3.6% +C methylated in Unknown context (CN or CHN): 13.4% + + +Bismark completed in 0d 0h 0m 8s