Limit of FIMO ouput

[Aoi Summer]

I used FIMO to find motifs in whole genome and set p-value threshold to 1.0E-4, but it seemed the limit of FIMO output text was 80,000 rows.

What can I do to get the whole result except to divide it.

THANKS!

[CharlesEGrant]

Using a p-value threshold when scanning an entire genome runs into the problem of multiple testing. It probably doesn't make sense to scan a full genome with a p-value of 1e-4. Most of those 80,000 rows will simply be chance matches to the motif and not biologically relevant.

These postings on the MEME Q&A site may be helpful:

Scanning genome sized datasets with FIMO

What should I use as a threshold of significance for q-value?

q-values in FIMO