eregenyi

Q: What parameters would you recommend optimizing, and what could be the reason for some peaks not being called?

7

Hi Taoliu, I am using macs2 for CUT&RUN transcription factor peaks. My biologist colleagues pointed out some peaks that are not called, but are visible in the rpm-normalized bedgraph visualization,...

Q: The number of reported differential peaks is much lower than the number of originally called peaks: Why?

1

Hi Taoliu, I am comparing two transcription factor's peaks. I analyzed unique peaks, meaning peaks that had no overlap (0 overlapping bases) between the two TFs. I was also interested...

Hi, I'm a junior bioinformatician, and used the package to annotate some peaks. The strand information is of 1, 2 format, and as I was used to the 0, 1,...

Hi, I have been going through the source code of the function gene.relative.velocity.estimates() to understand better the way velocities are calculated. As I see, the velocity is estimated by the...