Motif Database about maggie

[zeyang-shen]

Of course you can use your own motif database!

The default motif database is the core vertebrates redundant JASPAR database under the data folder of our repository. All the motif files were originally downloaded from the JASPAR website in the JASPAR format. See an example here for SPI1 motif: MA0080.4.jaspar. JASPAR format stores counts, so if you start with probabilities, you can convert probabilities to counts by multiplying a large number (e.g., 1000).

If you happen to have motif files in the HOMER format, we have a custom function to convert HOMER motif files to JASPAR format:

maggie/maggie/utils.py

Line 299 in 8087820

def jaspar2homer(homer_file, output_file):