Blacklist for bacterial genome [ChIPseq]?

Question

[Emily Wasson]

Hi there,

I am working on a ChIPseq experiment with bacteria. I have the following questions:

1) Is blacklisting such a small genome necessary for a ChIPseq analysis (4.4 Mbp)? 2) Does ENCODE only provide blacklists for model organisms (mouse, fly, human, worm)? 3) Is there any way to obtain or create blacklists for non-model species?

Would appreciate some advice tremendously :)

[Papyrus]

One thing you could do if you have Input samples is to define a experiment-specific blacklist (a.k.a. "greylist") (e.g. with this package by looking at regions of enrichment in the Input). Though as it is such a small genome I'd proceed with caution, and you're almost close to being able to directly examine the whole genome in a browser to check for artifacts.

[Emily Wasson]

That makes sense, thank you for the explanation and thank you so much for sharing the package!

[ChuYi]

Hi, have you figured out how to generate blacklist regions?

[Ram]

Please do not add answers unless you're answering the top level question. Instead, use Add Comment or Add Reply as appropriate. I've moved your post to the right location this time, please be more careful in the future.

Answer 1

[ATpoint]

I do not think that a blacklist depends on genome size. Blacklisted regions are those that (regardless of the specific protein target/antibody) always attract reads and form peaks, for example because they attract spurious mappings. That though you would only know if you have many datasets from that bacterium and could therefore identify these consistently-enriched regions. If you don't have that, then you probably cannot make a reliable blacklist. ENCODE to my knowledge has NGS blacklists for very few models (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) but not any bacteria. That means you probably have to accept the peak lists you get. Others might have different opinions.