Mercurial > repos > bgruening > bismark
diff 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 |
|---|---|
| date | Tue, 30 Jul 2019 10:33:02 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_report_mate.txt Tue Jul 30 10:33:02 2019 -0400 @@ -0,0 +1,42 @@ +Bismark report for: input1_fq_1.fq and input1_fq_2.fq (version: v0.22.1) +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 +Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) + +Final Alignment report +====================== +Sequence pairs analysed in total: 1000 +Number of paired-end alignments with a unique best hit: 0 +Mapping efficiency: 0.0% +Sequence pairs with no alignments under any condition: 1000 +Sequence pairs did not map uniquely: 0 +Sequence pairs which were discarded because genomic sequence could not be extracted: 0 + +Number of sequence pairs with unique best (first) alignment came from the bowtie output: +CT/GA/CT: 0 ((converted) top strand) +GA/CT/CT: 0 (complementary to (converted) top strand) +GA/CT/GA: 0 (complementary to (converted) bottom strand) +CT/GA/GA: 0 ((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: 0 + +Total methylated C's in CpG context: 0 +Total methylated C's in CHG context: 0 +Total methylated C's in CHH context: 0 +Total methylated C's in Unknown context: 0 + +Total unmethylated C's in CpG context: 0 +Total unmethylated C's in CHG context: 0 +Total unmethylated C's in CHH context: 0 +Total unmethylated C's in Unknown context: 0 + +Can't determine percentage of methylated Cs in CpG context if value was 0 +Can't determine percentage of methylated Cs in CHG context if value was 0 +Can't determine percentage of methylated Cs in CHH context if value was 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