Mercurial > repos > bgruening > bismark
diff test-data/mapping_report.txt @ 8:9bfe38410155 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author | bgruening |
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date | Wed, 22 Aug 2018 08:09:42 -0400 |
parents | |
children | f211753166bd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_report.txt Wed Aug 22 08:09:42 2018 -0400 @@ -0,0 +1,42 @@ +Bismark report for: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat (version: v0.20.0) +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 /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ 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: 44115 +Number of alignments with a unique best hit from the different alignments: 554 +Mapping efficiency: 1.3% +Sequences with no alignments under any condition: 43115 +Sequences did not map uniquely: 446 +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: 230 ((converted) top strand) +CT/GA: 324 ((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: 8563 + +Total methylated C's in CpG context: 245 +Total methylated C's in CHG context: 51 +Total methylated C's in CHH context: 114 +Total methylated C's in Unknown context: 1 + +Total unmethylated C's in CpG context: 133 +Total unmethylated C's in CHG context: 1762 +Total unmethylated C's in CHH context: 6258 +Total unmethylated C's in Unknown context: 5 + +C methylated in CpG context: 64.8% +C methylated in CHG context: 2.8% +C methylated in CHH context: 1.8% +C methylated in Unknown context (CN or CHN): 16.7% + + +Bismark completed in 0d 0h 0m 8s