Results for "Command lines"
Bio-Scripts
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 #...2523 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses p...'trimlimit=i', 'prefix=s'); # process remaining command line arguments (hopefully onl...=> 1, -message => "Error: Unknown comma...2308 days ago
Remove duplicate lines with perl
#! perl -sw use strict; my %lines; #open DATA, $ARGV[0] or die "Couldn't open $ARGV[0]: $!\n"; while () { print if not $lines{$_}++; } __DATA__ apple apple plum vinegar apple banana banana banana apple2293 days ago
Extract the values between to user defined string with Perl
#!/usr/bin/perl -w use strict; while () { process..._ XXXX YYYY START These are the first set of lines which are to be extracted E...XXX ZZZ YYY START These are the second set of lines which are to be extracted E...2293 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2264 days ago
- You have to compile the code with a C++ compiler. TDM-GCC MinGW compiler which you can download from this l...e cmd, navigate to the folder containing the .cpp files using the "cd" command, and then execute these comma...
850 days ago
Plot custom gene density with R
library(karyoploteR) pp2250 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2154 days ago
- ...ng for grep that handles long lines and -e... /bin/grep checking f...ig.status: executing depfiles commands make all-recursive make[1...ng for grep that handles long lines and -e... /bin/grep checking f...ig.status: executing depfiles commands configure: WARNING: unrec...
2151 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages jit@jit-H...process is completely automated, unless you passed in the `--ask' flag on the comma...1537 days ago
