Reproducing ScreenGeneEffectUncorrected and CRISPRGeneEffectUncorrected from 25Q3

Q&A
1

Greeting,

I am trying to reproduce the scores listed in ScreenGeneEffectUncorrected.csv and CRISPRGeneEffectUncorrected.csv from the RawReadcounts.

I have ran `chronos` with 1201 epoches, but my results tend to be slightly different.

I have come to the conclusion that it might be because I might be missing a step or two in the pre-processing of the readcounts before running chronos.

It is possible that my implementation of the Achilles pipeline might be flawed.

Do you by any chance have an implementation of such pipeline that you can share?

Thanks

2

Hi zancoste,

We are working on creating a public version of the Achilles pipeline. Although it won’t be runnable without access to our internal data ecosystem, it will at least lay out the steps the data goes through. In the meantime, I suggest 1) make sure you have the latest version of the master from GitHub, 2) have excludes replicates and screens that fail QC, and 3) compare the precorrection version of your gene effects to the CRISPRGeneEffectUncorrected file, since there are subtleties in the postcorrection steps that could easily lead to different results.