SergioRodLla

Hello, I have the same issue. Did you manage to get insights on this?

Hi @WJH58, I wonder if you have gained more insights regarding this. How did you generate the bigwig file you used for IGV? Is this better than using the gappedPeak...

Hello, RXCoux. I have the same problem and from what I understand the problem comes from the argument `asMates=TRUE` in the `readBamFile()` function. If it is set to `FALSE` ,...

Hi @RXCoux , did you use `TSSEscore()` with the default arguments? If so then the scores you get may be smaller than expected if you are comparing to the ATAC-seq...

Hi @jianhong , thank you for the answer. I am having problems to interpret how they compute the TSSEscore according to the ENCODE standards. Because they don't mention the width...

Happy new year! Thank for the information. I just want to mention the following: I have been looking at the code of the function and although I do not understand...

Hello, I saw that some papers in which they use macs2 for ATAC-seq they previously filter the fragment sizes to get a set corresponding to nucleosome free regions (NFR) and...

Hi! I was about to try to do the same. If your images are in NIfTI format I would suggest to read them with nibabel, convert then to numpy arrays,...