Results for "chromosome"
Bio-Scripts
...rict; use warnings; use LWP::Simple; use XML::XPath; use XML::XPath::XMLParser; # Use DAS of UCSC to fetch specific sequence by its given chromosome position # From here: https:...2901 days ago
Blast script to index and extract sequence !!
...11353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCAT...11353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome AGCTTTTCATT...100-105 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome TTAAAA2843 days ago
Perl script to insert the DNA string in genome
...; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fasta file my $chr="test"; #insertion chromosome my $pos=10; # position of th...2650 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted by...2305 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() ; $R->startR ;...2290 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, load it, # if not, install and load it if("ggplot2" %in% rown...2275 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here...2131 days ago
- #!/usr/bin/env Rscript library(RCircos) # usage: Rscript make_circos.r # parse args args = commandArgs(trailingOnly=TRUE) sv.file
290 days ago
Raku script to find overlaps between two bed files !
...$line2.split("\t"); my $chr2 = @fields2[0]; my $start2 = @fields2[1]; my $end2 = @fields2[2]; # Check for chromosome match and overlap if...85 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '85 days ago
