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This analysis helps you compare two files that contain gene names.
Thus, using the script that follows, one can find the common genes (some of the detected peaks where found in their promoters) between two different ChIPseq runs.
To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH. Read How to set the CHIPSEEQERDIR variable.
1. Type the command:
CompareGenes.pl --input1=file1 --input2=file2 --keepUniqRec=1 --output=YOUR_DESTINATION_FOLDER
keepUniqRec=INT if set to 1 keeps a gene only once. Default is 0. output=STR path to the desired destination folder
2. See the results.
The results are 4 files inside the directory of file1 and file2. One file shows the unique genes from file1, another the unique genes from file2, a third one the unique genes from both files, and a last file shows the genes that were common.