Mercurial > repos > big-tiandm > mirplant2

comparison quantify.pl @ 44:0c4e11018934 draft

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Uploaded
author big-tiandm
date Thu, 30 Oct 2014 21:29:19 -0400
parents a79212816cbc
children ca05d68aca13
comparison
equal deleted inserted replaced
43:4c0b1a94b882 44:0c4e11018934
420 close IN; 420 close IN;
421 } 421 }
422 sub mapping{ 422 sub mapping{
423 my $err; 423 my $err;
424 ## build bowtie index 424 ## build bowtie index
425 print STDERR "building bowtie index\n"; 425 #print STDERR "building bowtie index\n";
426 $err = `bowtie-build $pre_file_name miRNA_precursor`; 426 $err = `bowtie-build $pre_file_name miRNA_precursor`;
427 427
428 ## map mature sequences against precursors 428 ## map mature sequences against precursors
429 print STDERR "mapping mature sequences against index\n"; 429 #print STDERR "mapping mature sequences against index\n";
430 $err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature mature_mapped.bwt`; 430 $err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature > mature_mapped.bwt 2> run.log`;
431 431
432 ## map reads against precursors 432 ## map reads against precursors
433 print STDERR "mapping read sequences against index\n"; 433 #print STDERR "mapping read sequences against index\n";
434 $err=`bowtie -p $threads -f -v $mismatch -a --best --strata --norc miRNA_precursor $read --al mirbase_mapped.fa --un mirbase_not_mapped.fa read_mapped.bwt `; 434 $err=`bowtie -p $threads -f -v $mismatch -a --best --strata --norc miRNA_precursor $read --al mirbase_mapped.fa --un mirbase_not_mapped.fa > read_mapped.bwt 2> run.log`;
435 435
436 } 436 }
437 437
438 sub subseq{ 438 sub subseq{
439 my $seq=shift; 439 my $seq=shift;