# Reproducing ScreenGeneEffectUncorrected and CRISPRGeneEffectUncorrected from 25Q3

**URL:** <https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572>\
**Category:** Q&A\
**Created:** [January 29, 2026, 2:19pm UTC](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572 "2026-01-29T14:19:06Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![zancoste](https://avatars.discourse-cdn.com/v4/letter/z/b9e5f3/32.png) [@zancoste](https://forum.depmap.org/u/zancoste)\
**Post date:** [January 29, 2026, 2:19pm UTC](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572/1 "2026-01-29T14:19:06Z")

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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

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**Author:** ![Joshua\_Dempster](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/joshua_dempster/32/19_2.png) [@Joshua\_Dempster](https://forum.depmap.org/u/Joshua_Dempster)\
**Post date:** [February 12, 2026, 3:06pm UTC](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572/2 "2026-02-12T15:06:11Z")

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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.

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**Author:** ![yejie\_yun](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yejie_yun/32/915_2.png) [@yejie\_yun](https://forum.depmap.org/u/yejie_yun)\
**Post date:** [April 7, 2026, 6:44pm UTC](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572/3 "2026-04-07T18:44:26Z")

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Hi zancoste,

Below is the link to the public version of the Achilles pipeline. Although it cannot be run without access to our internal database, it includes all data processing steps. [GitHub - broadinstitute/achilles-pipeline-2.0-public · GitHub](https://github.com/broadinstitute/achilles-pipeline-2.0-public)