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
date Wed, 22 Aug 2018 08:09:42 -0400
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
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+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