MEME-Chip output lacks motif names

Question

[Sadia]

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.

[Sadia]

Thank you Gautier. I was missing the information in the command.

Answer 1

[Gautier Richard]

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

[chrisclarkson100]

@Gautier Richard Hi this is quite useful thank you however I am confused about specifying the database using the link that you supplied above:

meme-chip -oc out seqs.fa

The above takes a relatively short time but the discovered motifs lack names as mentioned in the question.

However when I download your database and retry:

wget  http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.18.tgz
tar -xvf motif_databases.12.18.tgz
meme-chip -oc out -db motif_databases/MOUSE/ seqs.fa

Redoing with a database (mouse as my data are from mouse) specified has been running 4 hours and still going.... Should I expect this/ is my path to the database wrong..? The motif that I expected to show up was discovered by the original way that didn't use a database- all I need is for it to name the motif now.... but this seems to be taking a really long time...

[chrisclarkson100]

I found out the answer to this question from : meme-chip command line usage error The following worked:

meme-chip -oc out -db motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme -db motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_redundant.meme seqs.fa