Create genome scaffolding with Perl
...($b1 eq "N") || ($b2 eq "N")) ? " " : "*"); } ############### Program starts here # set default...ading query sequences into memory..."); open(my $queryFile, "=21 tab-separated values, got %d)",...2345 days ago
Plot the clock using Lastz -gerenal outfile
use strict; use warnings; use Statistics::R ; use List::Util qw(sum); #Usage perl clockPlot.pl Palindrome.palfc 1500 my $R = Statistics::R->new() ; $R->start...2335 days ago
Extract the values between to user defined string with Perl
...rintout spacer for next record } __DATA__ XXXX YYYY START These are the first set of lines which are to be extracted END START New line And new Will be extracted? END XXX ZZZ YYY STA...2329 days ago
Plot the density of genes in R
...l and load it if("ggplot2" %in% rownames(installed.packages())){ library(ggplot2) } else { install.packages("ggplot2") library(ggplot2) } # import a t...2320 days ago
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Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { chomp; n...2287 days ago
Perl script to convert fastq to fasta file
...a"; my $infile = shift or die $usage; my $outfile = shift or die $usage; my $factory = Bio::Factory::EMBOSS->new; my $seqret = $factory->program('seqret'); # $seqret is a Bi...2287 days ago
Plot custom gene density with R
library(karyoploteR) pp2286 days ago
Estimate Genome Size with Jellyfish and R
...of treads to be used in the run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m -mer-len=unit32...30 jellyfish histo -o 19mer_out.histo 19mer_out #Plot dataframe19...2282 days ago