FIMO weird score values in fimo.tsv

[Petr]

Hi,

I face an issue when trying to parse fimo.tsv, the score column contain something what is not number:

motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence
GCTGCYGCCRYC 5 ENSG00000108298.12|ENST00000225430.9|protein_coding|RPL19 51 62 + XII.77 4.23e-05 0.0238 GCGGCCGCAGCC

CTCTTTCCGTYCCCSGG 6 ENSG00000114391.14|ENST00000394077.8|protein_coding|RPL24 21 37 + -3.70707 0.000176 0.0663 GTCTTTCCGTGGAGCTG

What does XII.77 mean, how do i interpret it? Also i noticed that some motif occurences have negative score, see second row, is this intentional, if so what does that mean?

Thanks for response

[cegrant]

Hi Petr,

That's an unexpected outcome. Certainly not one we've ever seen before the XII looks like a chromosome number which would usually be part of the sequence name. Could you forward us copies of your input sequence and motif files? That will allow us to try to sort out the problem.