comparison quantify.pl @ 44:0c4e11018934 draft

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43:4c0b1a94b882

	close IN;
}
sub mapping{
    my $err;
## build bowtie index
    print STDERR "building bowtie index\n";
    $err = `bowtie-build $pre_file_name miRNA_precursor`;

## map mature sequences against precursors
    print STDERR "mapping mature sequences against index\n";
	$err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature mature_mapped.bwt`;

## map reads against precursors
    print STDERR "mapping read sequences against index\n";
    $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 `;

}

sub subseq{
	my $seq=shift;

44:0c4e11018934

	close IN;
}
sub mapping{
    my $err;
## build bowtie index
    #print STDERR "building bowtie index\n";
    $err = `bowtie-build $pre_file_name miRNA_precursor`;

## map mature sequences against precursors
    #print STDERR "mapping mature sequences against index\n";
	$err = `bowtie -p $threads -f -v 0 -a --best --strata --norc miRNA_precursor $mature > mature_mapped.bwt 2> run.log`;

## map reads against precursors
    #print STDERR "mapping read sequences against index\n";
    $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`;

}

sub subseq{
	my $seq=shift;