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Revision as of 12:43, 12 December 2014
, 12:43, 12 December 2014→Visualizing Ancestry
__TOC__
== Setup ==
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''If you are already logged in, you can skip this section.''
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{{SeqShopLogin}}
{{SeqShopLogin}}
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== Setup your terminal ==
Resume screen:
screen -r
== Setup ==
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''If you were sequenced, set these values:''
'''Only if your snpcalling is still running, let Mary Kate know, expand, and follow these instructions'''
export SAMPLE=Sample*
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* Detach from screen
Ctrl-a d
* Start new screen
screen
* Reset environment variables (replace SampleXX with your sample name)
export SAMPLE=SampleXX
source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
* When you detach from screen and reattach, you will have multiple screen sessions
** The ancestry one will have today's date, the snpcall one will have an earlier date.
*** Mary Kate can explain how to reattach to a specific session when we get there.
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'''Instructions for everyone: Setup LASER'''
Source the LASER setup:
source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt
source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt
(SAMPLE & OUT were previously set in your screen session.)
After setting this, also do
After setting this, also do
This step takes ~1 hour for a genome sequenced at 17X.
This step takes ~1 hour for a genome sequenced at 17X.
While this is running, we will go look at other results, so exit screen:
Ctrl-a d
While that's running, let's go run the Association Analysis Practical: [[SeqShop: Genetic Association Analysis Practical, December 2014]]
=== Checking if Pileup finished ===
screen -r
'''Did everyone's finish?'''
If not, let's go to Indel: [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]]
If yes, let's continue below:
=== Step 2: pileup --> seq ===
=== Step 2: pileup --> seq ===
== Visualizing Ancestry ==
== Visualizing Ancestry ==
Change to that new directory:
Change to that new directory:
Take a look:
Take a look:
evince Results_on_HGDP.pdf &
evince Results_on_HGDP.pdf &
== Return to Calling your own Genome ==
Go to [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]] and pick up where we left off.
