3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Unix
* 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 =
=== 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]
* [http://genome.sph.umich.edu/wiki/GLF GLF]
