Mercurial > repos > big-tiandm > mirplant2
comparison matching.pl @ 44:0c4e11018934 draft
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author | big-tiandm |
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date | Thu, 30 Oct 2014 21:29:19 -0400 |
parents | 7321a6f82492 |
children | c75593f79aa9 |
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43:4c0b1a94b882 | 44:0c4e11018934 |
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42 `bowtie-build $genome $genome`; | 42 `bowtie-build $genome $genome`; |
43 $index="$genome"; | 43 $index="$genome"; |
44 } | 44 } |
45 | 45 |
46 ### genome mapping | 46 ### genome mapping |
47 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa --max genome_mapped_Mlimit.fa > genome_mapped.bwt`; | 47 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa --max genome_mapped_Mlimit.fa > genome_mapped.bwt 2> run.log`; |
48 | 48 |
49 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`; | 49 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`; |
50 | 50 |
51 sub Time{ | 51 sub Time{ |
52 my $time=time(); | 52 my $time=time(); |