Obtaining individual TF binding sites from MCAST local runs

[María José Delgado]

Hi!

I am running MCAST locally (MEME Suite via Bioconda) and I was wondering whether it is possible to obtain the individual motif binding sites (TFBS) predicted within each cluster as a GFF (or similar) output.

I am aware that the web interface displays individual motif matches in the HTML output, but extracting their genomic coordinates one by one from the HTML is quite cumbersome, and having them directly as a structured file would be very useful for downstream analyses.

At the moment, the local mcast.gff seems to report only cluster (CRM) coordinates, not the individual motif hits.

As a workaround, I am running FIMO with the same motif set and p-value threshold and intersecting the hits with MCAST clusters.
Would this be considered a reasonable and comparable approach, or is there a recommended way to obtain motif-level information directly from MCAST?

Thanks in advance!

Majo