Elementolab/make PAGE input
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This analysis helps you create an input file for PAGE, given a list of genes.
To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.
1. First extract the genes, after running ChIPseeqerAnnotate
Learn how to do this here
Let's say you'll end up with the file geneslist.txt that will contain the ORF names of the genes.
2. Type the command:
make_PAGE_input.pl --geneslist=geneslist.txt [OR --geneslistFolder=FOLDER] --refgene=DATA/hg18/refSeq
3. See the results.
The output of the script is an ORF.txt file that can be directly used in PAGE (see step 2 in Elementolab/ChIPseeqer_2iPAGE)
IMPORTANT: The input file names must not contain the word "ORF".