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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 to use git
* [[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 in [[http://genome.sph.umich.edu/wiki/Main_Page]]).
= Unix =
= 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.]]
CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
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 =
= Resources =
= Resources =
== Nex-Gen Sequencing (NGS) ==
=== Nex-Gen Sequencing (NGS) ===
==SAM/VCF format documentation ==
SEQAnswer forum [[http://seqanswers.com/ Homepage ]]
RNAseq blog [[http://rna-seqblog.com/ Homepage ]]
=== 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]]
Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]]
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]
