stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

arq5x

# assumes you have SSH'ed and qlogin'ed
cd thu
cd mydata

# slide 5
curl https://s3.amazonaws.com/gemini-tutorials/trio.trim.vep.vcf.gz > trio.trim.vep.vcf.gz
curl https://s3.amazonaws.com/gemini-tutorials/dominant.ped > dominant.ped
gemini load --cores 2 \
              -v trio.trim.vep.vcf.gz \
              -t VEP \

nilesh-tawari

-- [[ Cheatsheet for LUA from http://www.newthinktank.com/2015/06/learn-lua-one-video/]]

-- Prints to the screen (Can end with semicolon)
print("Hello World")

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Multiline comment
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-- Variable names can't start with a number, but can contain letters, numbers