Mercurial > repos > big-tiandm > sirna_plant

comparison matching.pl @ 13:a8c011dc575b draft

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author big-tiandm
date Wed, 29 Oct 2014 04:19:42 -0400
parents 07745c0958dd
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12:318617877a10 13:a8c011dc575b
37 `bowtie-build $genome genome`; 37 `bowtie-build $genome genome`;
38 $index="genome"; 38 $index="genome";
39 } 39 }
40 40
41 ### genome mapping 41 ### genome mapping
42 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa > genome_mapped.bwt`; 42 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa > genome_mapped.bwt 2> run.log`;
43 43
44 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`; 44 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`;
45 45
46 sub usage{ 46 sub usage{
47 print <<"USAGE"; 47 print <<"USAGE";