Mercurial > repos > big-tiandm > sirna_plant

comparison rfam.pl @ 12:318617877a10 draft

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author big-tiandm
date Wed, 29 Oct 2014 04:19:04 -0400
parents 07745c0958dd
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11:a0222bdfe2ac 12:318617877a10
40 $index="rfam"; 40 $index="rfam";
41 } 41 }
42 42
43 #chdir "rfam_match_1397022331"; 43 #chdir "rfam_match_1397022331";
44 ### genome mapping 44 ### genome mapping
45 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`; 45 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt 2> run.log`;
46 46
47 sub checkACGT{ 47 sub checkACGT{
48 my $string; 48 my $string;
49 open IN,"<$rfam"; 49 open IN,"<$rfam";
50 while (my $aline=<IN>) { 50 while (my $aline=<IN>) {