Introduction to new students

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Introduction to New Students

Programming

  • R/C++/perl/python code snipplets / toy examples of various packages

[Internal Resources]

  • How To Use Git : Git is a version control software. We have useful library codes and useful applications (see Sequence Analysis Tools section on the Main_Page).

Unix

Basic Unix/Linux Intro

Screen Commands - use screen to save a session even when you log off

CSG Documentation [AWK, BASH, UNIX commands and etc.]

Git [How to use git ], [PDF presentation], [Cheatsheet]

Tools

Samtools [Manual]

PLINK [Homepage]

MERLIN [Homepage]

BWA[Homepage ]

Resources

Nex-Gen Sequencing (NGS)

SEQAnswer forum [Homepage ]

RNAseq blog [Homepage ]


Data File Formats

We work with the following formats:

SAM/VCF format documentation

[SAM specification]

[VCF specification]

Group Chat [instant Messaging]

Lecture Materials

Lecture Notes for Goncalo's Introductory Genetics Course Biostatistics 666

Web-seminars on next generation sequencing and related topics Newton Institute Workshop