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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
author bgruening
date Thu, 01 Aug 2019 10:47:13 -0400
parents b6aa3b6ba129
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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


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