AswinSSoman

1. Install Samtools

• Samtools is a suite of programs for interacting with high-throughput sequencing data.

• Download samtools-1.9, bcftools-1.9, htslib-1.9 from htslib.org

• First install htslib-1.9

• Unzip & go inside htslib folder in terminal and type the following.

  ./configure
   make
   sudo make install
  

AswinSSoman

1. Install BWA From Github

• git clone bwa repository from github/lh3
• Go inside downloaded bwa folder: cd bwa
• Recompile the pieces of the program using command: make

2. Download Lambda phage reference genome from ncbi

• 2.1 Manual downloading
  • Search lambda phage in Genome database.
  • Click on Genome Assembly and Annotation report.
• Click on NC_001416.1 on segments.

AswinSSoman

Basics of Linux

This guide is designed to help new users understand the more important aspects of Linux. It is not meant to be an exhaustive tutorial, but rather a primer.

---

Introduction

Linux (or GNU/Linux) isn't one singular operating system as many people believe it to be, but rather a broader term for a large number of operating systems built using the Linux kernel. These different operating systems are referred to as distributions or "distros". Different Linux distributions use the same mostly the same software but are packaged and setup differently. Many, if not most, distros are based of off other more popular distros. The major differences that the average user notices are in what desktop environment the distro uses, and how/where software is managed and installed from.

AswinSSoman

FILES

mkdir - create directory

touch 1.txt - create file

touch {1,2,3}.txt - create 1.txt 2.txt and 3.txt

rm - remove file or dir

AswinSSoman

1. To put an image from internet link.

1.1 To just place an image (with native resolution).

Use this command :

![Infinity War](https://i.redd.it/4y4m7jl5yfbz.jpg)

 

AswinSSoman

AswinSSoman

- Headers

# This is an <h1> tag         
## This is an <h2> tag        
###### This is an <h6> tag     

- Emphasis

AswinSSoman

Objective - To analyze how the detection of relaxed selection of CYP8B1 gene by RELAX is affected by the following :

• number of gaps
• length of gaps
• number of species

Steps - MSA's and Tree Building

• 1. Select the order and number of species to be used.

AswinSSoman

#!/bin/env perl

use strict;
use warnings;

use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Scalar qw(wrap_array);
use IO::String;

AswinSSoman

Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

[samtools]