Introduction to new students

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 in [[1]]). A dedicated introduction page is here: [How to use git]

Unix

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:

• FASTQ - used to store sequence reads and their quality scores
• SAM/BAM - used to store additional information from what is in a FASTQ file, possibly including alignment information
• VCF: https://statgen.sph.umich.edu/wiki/VCF_4.0
• GLF

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