ATAC-seq transcription factor binding prediction

Question

[Lucy]

Hi,

I am trying to predict transcription factor binding sites from ATAC-seq data, for which I also have matched RNA-seq. I have read a lot of papers recently suggesting different methods for doing this (all of which claim that they are better than the other techniques). I was wondering whether anyone had experience with these different methods, and whether they would recommend any?

I am very confused by all of the available options so would appreciate some guidance!

Thanks,

Lucy

[am2622]

Hi Lucy I am going through the same process, have you found a good software to start with?

Thanks,

Anyi

[Lucy]

I still haven't worked out the best way to do this. Have you had any luck?