Results for "rna-seq"
Bio-Scripts
#!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #transcribe DNA to RNA - T changes to U my $RNA = $DNA; $RNA =~ s/T/U/g; print "RNA sequenc...2908 days ago
Check if your coputer ready to use BioPerl
#!/usr/bin/perl use strict; use warnings; #bioperl example code use strict; use warnings; #make the bioperl module (class) accessible to your program use Bio::Seq; print"ok - ready to use Bio::Seq";2908 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n". " -h: help\n". " -m: missing character\n". "Print out the name of...2905 days ago
- #!/usr/bin/env perl use strict; use warnings; use LWP::Simple; use XML::XPath; use XML::XPath::XMLParser; # Use DAS of UCSC to fetch specific sequence by its...
2901 days ago
Count GC Content in nucleotide sequence with Perl
#!/usr/bin/perl -w ### Usage: get_gc_content.pl ### #-----------------------------------------------------...2896 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extractS...2866 days ago
Perl script introduces control structures, arrays and hashes.
#!/usr/bin/env perl use strict; use warnings; my @first_array = ('DNA', 'ATGCGTGC', 5, 'RNA', 'AUGC'); print $first_array[0], "\n\n"; # Scalar gives actual s...2853 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->n...2618 days ago
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CONTIG , $LOC , -l...2699 days ago
- #! /usr/local/bin/perl5.8.3 -w ### ### Script Name : calcN50.pl ### Description : This script calculates the N50 of a collection of sequences in a fasta file ###...
2695 days ago
