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| = STOM 2014 Workshop - Practical Sessions = | | = STOM 2014 Workshop - Practical Sessions = |
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− | 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 the [[ http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344 | link]] | + | 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 |
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| 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 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. |
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| This page only covers lecture 2, 5, 6, 8 that are taught by Hyun Min Kang. | | This page only covers lecture 2, 5, 6, 8 that are taught by Hyun Min Kang. |
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− | == Lecture 2 ==
| + | 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 |
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− | * To see the files for the session, type
| + | Note that some commands can be very long and may go farther than the browser's width |
− | ls /data/stom2014/session2/
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− | If you see any errors, please let me know now!
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− | * For convenience, let’s set some variables
| + | == Lecture 2 : Genomic Control, PCA, EMMAX == |
− | export S2=/data/stom2014/session2 | + | |
− | mkdir ~/out
| + | Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_2 | Page for Practice 2 ]] |
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| + | == Lecture 5 : GotCloud Alignment Pipeline == |
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| + | Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_5 | Page for Practice 5 ]] |
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| + | == Lecture 6 : GotCloud Variant Calling Pipeline + samtools == |
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| + | Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_6 | Page for Practice 6 ]] |
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| + | == Lecture 8 : Sequence-based association using EPACTS == |
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| + | Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8 | Page for Practice 8 ]] |