Difference between revisions of "Introduction to new students"
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* R/C++/perl/python code snipplets / toy examples of various packages | * R/C++/perl/python code snipplets / toy examples of various packages | ||
[[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]] | [[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]] | ||
| − | * How | + | * [[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]]). |
| − | Git is a version control software. We have useful library codes and useful applications (see Sequence Analysis Tools section | ||
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= Unix = | = Unix = | ||
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| + | [[Basic Unix/Linux Intro]] | ||
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| + | [[Screen Commands]] - use screen to save a session even when you log off | ||
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 = | ||
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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] | + | * [http://en.wikipedia.org/wiki/FASTQ_format FASTQ] - used to store sequence reads and their quality scores |
| − | * [[SAM]]/[[BAM]] | + | * [[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 | * [[VCF]]: https://statgen.sph.umich.edu/wiki/VCF_4.0 | ||
| + | * [http://genome.sph.umich.edu/wiki/GLF GLF] | ||
=== SAM/VCF format documentation === | === SAM/VCF format documentation === | ||
Latest revision as of 21:39, 17 June 2014
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 on the Main_Page).
Unix
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:
- 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
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
