I've been going through HOMER for prediction of motifs in bacterial species such as Mycobacterium tuberculosis. I saw that HOMER doesn't have background database for any bacterial species:
Organism Mset human vertebrates mouse vertebrates rat vertebrates frog vertebrates zebrafish vertebrates fly insects worm worms yeast yeast arabidopsis plants
How to restrict the prediction for just bacterial species, so that HOMER result doesn't show motifs from other species?There's a '-bg' parameter in which we can give BED file for background. If I give Mycobacterium tuberculosis's GFF in '-bg' parameter, it will be biasing results just towards Mycobacterium tuberculosis itself.
Link - http://homer.ucsd.edu/homer/ngs/peakMotifs.html Please help. Thanks in advance.. :)