I want to know whether TRACE can be applied for fragmented plant genomes.

[Shokusei]

Hi, Boyle-Lab
I'm planning to use TRACE to determine plant cis factor TF binding.
And I'll use constructed de novo fragemnted genome of Mesembryanthemum crystallinum L.
According to your paper(https://www.biorxiv.org/content/10.1101/801001v1.full#ref-4), it seems that TRACE is suitable for only the human complete genome.
If you know the way to use TRACE for plant fragmented genomes, I would like you to tell me.
Best Regards.

[aboyle]

You should be able to use TRACE just fine on any genome, including a plant genome. The only change from the instructions here in github are that you will need a custom motif file (and cluster file if you want) using motifs from your organism (or maybe just general plant PWMs). See this section: https://github.com/Boyle-Lab/TRACE#build-an-initial-trace-model