outputs of different version of MEME suite

[Gnéré Mariame Coulibaly]

Hi,

Is it possible to obtain different output when using different version of meme?
I ran fimo last year with the default -thresh  1.0E-4. And the results are different from those that I have with the new version.
Could someone explain it to me please?

Thanks.

[cegrant]

You can consult the release notes to see what changes have been made to the MEME Suite tools.

It looks like there were a couple of changes to FIMO on August 24, 2023. Once change added an additional output file which shouldn't cause a mismatch with your results. However, we also made the parsing of genomic coordinates in sequence FASTA headers the default behavior for FIMO. Previously genomic coordinates in the header were only parse if the '--parse-genomic-coord' switch was given.

If the differences in your runs seem unrelated to this change, please forward us the HTML output file from both runs and we'll see if we can track the issue down.