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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+++ b/test-data/mapping_report_short.txt	Tue Jul 30 06:30:36 2019 -0400
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+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