Question about BLAT comparison for sequence similarity check

[XuanrZhang]

Hi @cameronraysmith，

Thanks for sharing DNA-Diffusion work.

I was wondering how you performed the BLAT comparison and what parameter settings you used when running BLAT.

For instance, I ran BLAT using blat test.fa generate.fa output.psl and calculated the longest match length. my results do not match yours. I suspect this may be due to differences in parameter settings. Could you share the parameters you used?

Additionally, when running BLAT on the same dataset, I consistently obtain a longest match length of 200, as it always finds the same sequence to match. Did you run BLAT for each CRE against the remaining CREs?

Thank you for your time and help!

Best, Xuan