54 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A...wo FASTA files # Last updated by: $Author$ # Last updated on...TA TC TG TT); # hashes for obersered and expected dinucleot...loop through sequence, take 2 bp and increment the hash count...loop through sequence, take 2 bp and increment the hash count...474 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745473 days ago
362 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems; my $total-bases = $sequence.chars;...174 days ago
Raku script to find SSRs in fastq file !
sub find-ssrs(Str $sequence) { my @ssr...{ my $repeat = $sequence.substr($min-repeats - 1, $max-rep...eats + 1; if $sequence.substr($max-repeat).index($repeat...} } return @ssrs; } sub process-fastq-file(Str $filen...174 days ago
Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) = @_;..._count = () = $sequence =~ /[GC]/g; my $total_bases = length($sequence); my $gc_content = ($gc_count / $total_bases) * 100; return $gc_c...158 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
#!/usr/bin/perl use strict; use warnings; sub multi_to_single_line_fasta { my ($input_filename, $output_filename) = @_; open my $input_file, '', $output_filename or die "Er...158 days ago
Bash script to convert Multi-line Fasta to Single-line Fasta !
#!/bin/bash input_filename="multi_line.fasta" output_filename="single_line.fasta" awk '/^>/ {printf("\n%s\n", $0);next; } { printf("%s", $0);} END {printf("\n");}...158 days ago
Bash script to calculate difference between column !
Space Separated awk '{ $5 = $2 - $4 } 1' inputput.txt > outdiff.txt Or with tab separation: awk 'BEGIN { OFS = "\t" } { $5 = $2 - $4 } 1' inputput.txt > outdiff.txt157 days ago