chrUn_gl000220

[Ishtiaque Hossain]

Hi,

So I ran ROSE on my H3K27Ac ChIP dataset on hESCs, and the program worked out as expected. I just have a couple things I want to clear up to make sure I understand things properly:

1. The program identified 64 super-enhancers, and the two papers associated with the code seem to identify a lot more super-enhancers. Is the low no. of super-enhancers due to a sub-standard ChIP (the MACS output identified around 5000 peaks) or something else?
2. The no. 1 ranked super-enhancer is chrUn_gl000220: 118992-145541. Do I remove this from the analysis since it maps to rRNA reads (and if so, at what step would you recommend), or do we include it in our analysis (it has a very high read compared to the other super-enhancers)?

Thank you.

‌