Difference between revisions of "Introduction to new students"

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(Data File Formats)
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CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
 
CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
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Git [[https://statgen.sph.umich.edu/wiki/How_To_Use_Git How to use git ]], [[https://statgen.sph.umich.edu/w/images/6/6b/2011_06_07_GitHowTo.pdf PDF presentation]], [[https://statgen.sph.umich.edu/w/images/c/c4/GitCheatSheet.pdf Cheatsheet]]
  
 
= Tools =
 
= Tools =

Revision as of 10:24, 29 June 2011

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:

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