Mercurial > repos > big-tiandm > mirplant2
comparison rfam.pl @ 44:0c4e11018934 draft
Uploaded
author | big-tiandm |
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date | Thu, 30 Oct 2014 21:29:19 -0400 |
parents | 9ae0d25e4169 |
children | c75593f79aa9 |
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43:4c0b1a94b882 | 44:0c4e11018934 |
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45 &checkACGT($rfam); | 45 &checkACGT($rfam); |
46 `bowtie-build $rfam $rfam`; | 46 `bowtie-build $rfam $rfam`; |
47 $index="$rfam"; | 47 $index="$rfam"; |
48 } | 48 } |
49 ### genome mapping | 49 ### genome mapping |
50 `bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`; | 50 `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`; |
51 | 51 |
52 sub checkACGT{ | 52 sub checkACGT{ |
53 my $string; | 53 my $string; |
54 open IN,"<$rfam"; | 54 open IN,"<$rfam"; |
55 while (my $aline=<IN>) { | 55 while (my $aline=<IN>) { |