(FIMO) How to run FIMO using a specific motif in the combined.meme output file?

[Leonardo Jo]

Hello everyone,

I recently ran MEME-ChIP to perform a de novo discovery analysis on different ChIP-Seq datasets,

That allowed me to identify three distinct motifs and their variations.

I was really satisfied with the result because those are the expected motifs.

I was hoping now to perform FIMO to identify the presence of these motifs in a different dataset, 

command:

> fimo combined.meme sequences.fa

However, FIMO is scanning all motifs at the same time when I use the combined.meme motif file.

I was wondering if there is a way to perform FIMO on only specific set of group of motifs in the meme-chip output (MEME, DREME, Centrimo), I tried the --motif option, and I wasn't able to make it work.
Do you guys know how to separate the meme output and create a .meme file for each one of the motifs identified?!

Thank you very much,

[cegrant]

I was wondering if there is a way to perform FIMO on only specific set of group of motifs in the meme-chip output (MEME, DREME, Centrimo), I tried the --motif option, and I wasn't able to make it work

The '--motif' option is the correct choice. You can repeat the option multiple times if you want to scan multiple motifs. For example

fimo --motif GTGATSDDBKTCACA --motif AACAATTTCA combined.meme sequences.fa

The strings after --motif should be the identifier for the motif.

If you post the command line you used we might be able to spot the problem.