Tutorial: EMMAX GotCloud STOM

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STOM 2014 Workshop - Practical Sessions

Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344

This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.

This page only covers lecture 2, 5, 6, 8 that are taught by Hyun Min Kang.

Here I assume that

  • The audience has basic knowledge of Unix system, basic utilities, and pipes
  • The audience has the account in the cluster system and know how to access to the resources presented here

Note that some commands can be very long and may go farther than the browser's width

Lecture 2 : Genomic Control, PCA, EMMAX

Please see Page for Practice 2

Lecture 5 : GotCloud Alignment Pipeline

Please see Page for Practice 5

Lecture 6 : GotCloud Variant Calling Pipeline + samtools

Please see Page for Practice 6

Lecture 8 : Sequence-based association using EPACTS

Please see Page for Practice 8