Additional info about how to use the software

[martynakgajos]

Hi, I have been using the server version for some time for motif discovery and I wanted to add the shell version to my pipeline. However, when I run:
BaMMmotif DIRPATH FILEPATH

I get the following message:

Error: No initial model is provided.

Am I missing some necessary step/required file?

[wge11]

Hi, BaMMmotif takes a PWM or binding sites as a seed for optimization. Thus you need to offer a PWM file or binding sites file as input. For generating a PWM file, you can use MEME or our PEnGmotif (link). After obtaining a MEME-like file, you can use it with the flag --PWMFile <MEME-like file> to refine it to a higher-order Markov model.

Hope this helps.