So, we performed an ShRNA screen targeting all kinases in the human genome in a ctrl and tumor cell. We want to look for which ShRNAs are important for the tumor cell viability and not the control one - basically a synthetic lethality shRNA screen. Each shRNA is barcoded. So when we finished the experiment we sent the samples for deep sequencing of the barcodes.

They sent us back excel files including the barcodes and the count of each one.

What I need to know is how do I deal with the multiple shRNAs targeting the same gene? Is there a way to take them all into consideration in the analysis?

All the online software do not take that into consideration since they suppose they're dealing with one gene input.

thanks