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Introduction to new students (view source)

Revision as of 21:39, 17 June 2014

883 bytes added ,  21:39, 17 June 2014
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Introduction to New Students
 
Introduction to New Students
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== Programming ==
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= Programming =
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== Unix ==
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== Tools ==
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== Resources ==
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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
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[[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]]
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* [[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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[[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]]
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= Unix =
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* How to use git
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Git is a version control software. We have useful library codes and useful applications (see Sequence Analysis Tools section in [[http://genome.sph.umich.edu/wiki/Main_Page]]).
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[[Basic Unix/Linux Intro]]
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A dedicated introduction page is here:
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[[Screen Commands]] - use screen to save a session even when you log off
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[[https://statgen.sph.umich.edu/wiki/How_To_Use_Git How to use git]]
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* Tools howto - with examples - samtools, PLINK, MERLIN, bwa, etc
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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]]
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= 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 ]]
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* SAM/VCF format documentation
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= Resources =
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=== Nex-Gen Sequencing (NGS) ===
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SEQAnswer forum [[http://seqanswers.com/ Homepage ]]
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RNAseq blog [[http://rna-seqblog.com/ Homepage ]]
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=== Data File Formats ===
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We work with the following formats:
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* [http://en.wikipedia.org/wiki/FASTQ_format FASTQ] - used to store sequence reads and their quality scores
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* [[SAM]]/[[BAM]] - used to store additional information from what is in a FASTQ file, possibly including alignment information
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* [[VCF]]: https://statgen.sph.umich.edu/wiki/VCF_4.0
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* [http://genome.sph.umich.edu/wiki/GLF GLF]
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=== 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]]
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* UNIX 101
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Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]]
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CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
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== Lecture Materials ==
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* Collection of useful resources/links
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Lecture Notes for Goncalo's Introductory Genetics Course [[Biostatistics 666]]
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Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]]
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Web-seminars on next generation sequencing and related topics [http://www.newton.ac.uk/programmes/CGR/seminars/index.html Newton Institute Workshop]
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1775...10871"

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