Hi all,

I'm new with using MACS and HOMER.  
I have created a bed file using MACS, and got 5 columns, for example:

    chr1	770811	771252	MACS_peak_1	93.92
    chr1	851512	851790	MACS_peak_2	57.31
    chr1	920907	921486	MACS_peak_3	207.37
    chr1	946784	946982	MACS_peak_4	73.24

Does anyone knows how can I create a column that contains the Unique Peak ID for HOMER analysis?
Also, What is the difference between using `findMotifs.pl` and `findMotifsGenome.pl` ? besides the fact that the first uses Unique Peak ID and the second uses genomic positions?

Appreciate your help!
The difference between `findMotifs.pl` and `findMotifsGenome.pl` is that the first works with gene names (or IDs) as input, and the second with genome coordinates. You have coordinates so you can use `findMotifsGenome.pl`.

For this you need a bed file, I think only the first 4 columns are needed (I am not sure though if the 5th is ignored automatically, or that you have to remove it yourself first). The unique peak ID is already in the 4th column.

Something like this will find the motifs of your peaks.

    findMotifsGenome.pl File_peaks.txt ~/Reference/hg38/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa File_peaks -p 20



