Normalization of read counts

[Karthikeyani Chellappa]

Hi 

We are interested in analyzing our CRISPR screen data sets in both PinAPL-PY and Mageck platforms. I read in Scientific Reports paper that there is high correlation in sgRNA identified by PinAPL-PY and Mageck analysis. 

We are interested in knowing how Mageck read-count was normalized. Nature Protocols published by Shirley Liu (2019) suggests normalizing data with either negative-control sequences (AAVS1) or nonessential genes  (list of 310 non-essential genes). 

We are curious to know if such normalization parameters can be included in the PinAPL-PY web application.

Thank you for you efforts in maintaining this webpage for use by Scientific community.

Thanks,

Karthi

[jianfeng huang]

Hi All,

I have the same question asked by Karthi two years ago, regarding the non-target control. 

Would PinAPL-PY, by default, normalize the target sgRNA counts (CPM) by the guide counts of non-target control from the same sample, as the MAGeCK does for data normalization? Is there an option in the advance setting to ask for such normalization with Non-Target control?

Many thanks in advance, highly appreciate any kind help!

Jianfeng