diff test-data/bismark_data.txt @ 0:8f25feb85166 draft

planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bismark_data.txt	Fri May 27 06:22:43 2016 -0400
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+Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0)
+Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)
+Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ 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:	316390
+Number of alignments with a unique best hit from the different alignments:	220558
+Mapping efficiency:	69.7%
+Sequences with no alignments under any condition:	93928
+Sequences did not map uniquely:	1904
+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:	108352	((converted) top strand)
+CT/GA:	112206	((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:	5291918
+
+Total methylated C's in CpG context:	465068
+Total methylated C's in CHG context:	1358074
+Total methylated C's in CHH context:	3449120
+Total methylated C's in Unknown context:	1499
+
+Total unmethylated C's in CpG context:	6399
+Total unmethylated C's in CHG context:	2988
+Total unmethylated C's in CHH context:	10269
+Total unmethylated C's in Unknown context:	454
+
+C methylated in CpG context:	98.6%
+C methylated in CHG context:	99.8%
+C methylated in CHH context:	99.7%
+C methylated in Unknown context (CN or CHN):	76.8%