FIMO: FIMO Output Format Differs between FIMO and MEME-ChIP

[i...@alum.mit.edu]

I ran FIMO within MEME-ChIP as well as FIMO on its own using MEME version 4.12.0.  The output file formats are not the same.

Here is an example line from the gff file of FIMO within MEME-ChIP:
chr11   fimo    nucleotide_motif        48033270        48033285        50.2    +       .       Name=GRGGWGKGGGHGGGRG_chr11+;Alias=MEME-1;ID=GRGGWGKGGGHGGGRG-MEME-1-1-chr11;pvalue=9.51e-06;qvalue= 0.0199;sequence=gagctgggggtggagt
Here is an example line from the gff file of FIMO run on its own:
chr1:13949-14010        fimo    nucleotide_motif        3       18      52.4    -       .       Name=3_chr1:13949-14010-;Alias=GRGGWGKGGGHGGGRG-MEME-1;ID=3-GRGGWGKGGGHGGGRG-MEME-1-1-chr1:13949-14010;pvalue=5.76e-06;qvalue= 0.0341;sequence=AAGGTGGGGGAGGTGA;

Here is an example of the fimo.txt file of FIMO within MEME-ChIP:
GRGGWGKGGGHGGGRG        MEME-1  chr1    3774725 3774740 +       18.1045 6.52e-10        0.00135 GAGGTGTGGGTGGGGG
Here is an example of the fimo.txt file of FIMO run on its own:
3       GRGGWGKGGGHGGGRG-MEME-1 chr8:56529540-56529710  3       18      -       22.197  5.42e-11        0.000203        GGGGTGGGGGCGGGGG

Is there a reason for this discrepancy?

Thanks so much!

[i...@alum.mit.edu]

It seems like the files have the same format if I run FIMO using the --parse-genomic-coord option.

[CharlesEGrant]

This is correct. MEME-ChIP automatically runs FIMO using the --parse-genomic-coord option. That option tries to parse genome coordinates from the sequence names, assuming they are using the UCSC sequence coordinates convention. If the --parse-genomic-coord option is not given, or if the sequence name doesn't seem to match the UCSC conventions, the first letter in the sequence is assumed to be at position 1.

There was a slight change to the FIMO plain text output in the 4.11.4 release. We added the 'alternate-id' column. The 4.11.4 versions of MEME and DREME identified motifs by their consensus sequence, as well as the order in which they were discovered.