Difference between revisions of "Introduction to new students"
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Introduction to New Students | Introduction to New Students | ||
| − | + | = Programming = | |
* 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]]). |
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| + | = Unix = | ||
| − | |||
| + | [[Basic Unix/Linux Intro]] | ||
| + | [[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.]] | |
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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 = | ||
Samtools [[http://samtools.sourceforge.net/samtools.shtml Manual]] | Samtools [[http://samtools.sourceforge.net/samtools.shtml Manual]] | ||
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BWA[[http://bio-bwa.sourceforge.net/bwa.shtml Homepage ]] | BWA[[http://bio-bwa.sourceforge.net/bwa.shtml Homepage ]] | ||
| − | * SAM/VCF format documentation | + | = Resources = |
| + | |||
| + | === Nex-Gen Sequencing (NGS) === | ||
| + | |||
| + | SEQAnswer forum [[http://seqanswers.com/ Homepage ]] | ||
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| + | RNAseq blog [[http://rna-seqblog.com/ Homepage ]] | ||
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| + | |||
| + | === Data File Formats === | ||
| + | We work with the following formats: | ||
| + | * [http://en.wikipedia.org/wiki/FASTQ_format 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 | ||
| + | * [http://genome.sph.umich.edu/wiki/GLF GLF] | ||
| + | |||
| + | === SAM/VCF format documentation === | ||
[[http://samtools.sourceforge.net/SAM1.pdf SAM specification]] | [[http://samtools.sourceforge.net/SAM1.pdf SAM specification]] | ||
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[[http://genome.sph.umich.edu/wiki/VCF VCF specification]] | [[http://genome.sph.umich.edu/wiki/VCF VCF specification]] | ||
| − | + | Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]] | |
| − | + | == Lecture Materials == | |
| − | + | Lecture Notes for Goncalo's Introductory Genetics Course [[Biostatistics 666]] | |
| − | + | Web-seminars on next generation sequencing and related topics [http://www.newton.ac.uk/programmes/CGR/seminars/index.html Newton Institute Workshop] | |
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
