Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory...g G mkdir "G$filename" cd "G$filename" # take action on each file. $f store current file name wget --i...2529 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory...mkdir "GFF$filename" cd "GFF$filename" # take action on each file. $f store current file name head -n...2520 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/Co...le..." ff=$(basename "${f%.*}") echo $ff # take action on each file. $f store current file name mkdir $f...2329 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower tha...= $i + 1; } $seq = "\U$seq"; # we are going to use the array @codons to store all of the codons in # the i...2152 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalRead...2138 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl...5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the ids if ($ARGV[1] eq "ids...2138 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
#Inspired from online search sudo apt-get update sudo apt-get install gcc sudo apt-get install make sudo apt-get install libbz2-dev sudo apt-get install zlib1g-de...1555 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing da...rs. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder....1540 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pr...b.pl at https://bioinformaticsonline.com/snippets/view/41440/perl-...$ ./web https://bioinformaticsonline.com #It return this W...pointment portal for all your medical needs like, online doctor appointment, Online boo...1509 days ago
Bash online to update Linux OS
sudo bash -c 'for i in update {,full-,dist-}upgrade auto{remove,clean}; do apt-get $i -y; done'688 days ago