Elementolab/Promoter Extraction

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you'll need to install both SNVseeqer and ChIPseeqer to run this analysis.

http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Install

http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNVseeqer_Install

Then (to extract 1kb promoters, upstream of TSS)

perl $CHIPSEEQERDIR/SCRIPTS/extract_upstream_sequence_coordinates_from_annotation.pl \ 
   --annotation=$CHIPSEEQERDIR/DATA/refGene.txt.07Jun2010.new --checkmaxlen=0 --lengthU=1000 --lengthD=0 > refgene1kproms.txt

Install the human genome (hg18) on your machine (you may have done it already); preferentially the repeat-masked version.

Possible source: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/

Quick install guide:

mkdir hg18/masked/
cd hg18/masked
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFaMasked.zip
unzip chromFaMasked.zip
cat *.masked > wg.fa.masked

Index the genome

$SNVSEEQERDIR/IndexFasta hg18/masked/wg.fa.masked

Extract seqs

$SNVSEEQERDIR/FastaExtract -fastafile hg18/masked/wg.fa.masked -intervals refgene1kproms.txt > refgene1kproms.seq
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