Question: MEME-Chip output lacks motif names
1
gravatar for Sadia
9 weeks ago by
Sadia40
Sadia40 wrote:

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.

chip-seq • 154 views
ADD COMMENTlink modified 4 weeks ago • written 9 weeks ago by Sadia40
1

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

ADD REPLYlink written 4 weeks ago by Sadia40
2
gravatar for Gautier Richard
4 weeks ago by
MPI IE, Freiburg, Germany
Gautier Richard240 wrote:

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

ADD COMMENTlink written 4 weeks ago by Gautier Richard240
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