Difference between revisions of "Introduction to new students"
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=== Data File Formats === | === Data File Formats === | ||
We work with the following formats: | We work with the following formats: | ||
| − | * [ | + | * [http://en.wikipedia.org/wiki/FASTQ_format FASTQ] |
| − | * [[SAM]] | + | * [[SAM]]/[[BAM]] |
| − | * [[VCF]] | + | * [[VCF]]: https://statgen.sph.umich.edu/wiki/VCF_4.0 |
=== SAM/VCF format documentation === | === SAM/VCF format documentation === | ||
Revision as of 17:52, 30 July 2010
Introduction to New Students
Programming
- R/C++/perl/python code snipplets / toy examples of various packages
- 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.]
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
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
