Generate the custom efficient motif set

[hahahafeifeifei]

Hi,
I want to follow the pipeline in vamos paper to generate the efficient motif set using my assemblies. Is there any software or script that can be used?

Thank you,
Fei

[Eric-Y-S]

I have the same need to create the efficient motif. If you have solved the problem, please let me know.

Thanks.

[BidaGu]

Hi,

We have since enhenced the framework for TR boundary and motif generation. You can find all scripts and a snakemake pipeline under https://github.com/ChaissonLab/vamos/blob/master/buildTRs. Please feel free to adapt any of the scripts for your own use.

The pipeline is somewhat complex. But you can find a description of the idea in this manuscript: https://www.biorxiv.org/content/10.1101/2024.08.07.607105v1