I've installed MEME locally. However, when I run meme-chip the output files do not assign known names to the motifs that were found. I know I am missing the database of motifs, but I'm not sure how to add this. Thank you for your help.
MEME-ChIP runs several tools like MEME and DREME to find motifs, and TOMTOM to assign such motif to known Transcription Factors. TOMTOM needs some motifs databases to run. To give motifs databases to MEME-ChIP so that TFs can be assigned to your enriched motifs found by MEME or DREME, you can use the following command line:
meme-chip -oc Analysis_1 -bfile background_sequences.mbm -db DB1.meme -db DB2.meme -db DB3.meme -db DB4.meme sequences.fa
The motifs databases can be downloaded here: http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.18.tgz