Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for genome assembly summary and extract the URL # USER need to...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/asse...al #Read the url from file and downlo...2538 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $...2537 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome_gff cd genome_gff # Look for genome assembly summary and extract the URL # USER need to...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/asse...l #Read the uerl from file and downlo...2529 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2344 days ago
Clump Finding Problem Solved with Perl
#Find patterns forming clumps in a string. #Given: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Genome. use strict; use warnings; my %myHash; my $string="CGGACTCGACAGAT...2340 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 name+location #GenomechrN...2320 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; us...f-mapped PSL file to scaffold a genome =head1 SYNOPSIS ./ps...s'); # process remaining command line a...-message => "Error: Unknown command-line option or "....nce is assumed to be forward strand...2315 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 i...2291 days ago
2271 days ago
Plot custom gene density with R
library(karyoploteR) pp2256 days ago