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lovisha aggarwal — Tue, 16 Sep 2025 20:00:15 -0000

Hello, I have 5 conditions set and each condition has 4 replicates. Adding to that pairwise sequencing is done so each replicate has forward and reverse fastq files. Do you have an idea if mageck would work in this dataset. if so how ? or should i run each replicate separately?

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Fiona Hartley — Wed, 24 Aug 2022 23:52:16 -0000

Hello,
I'm getting the following error message when running mageck test in --paired mode
"An error occurs while trying to compute p values. Quit.."
Up until then, the log file appears normal.

I can't figure out why this error is occurring. I'm trying to run analysis on x3 control and x3 treated samples. This error occurs if I try to run all the samples together (1+2+3), or if I try to run 1+3, leaving out sample 2. However, the program works fine if I run it on each sample individually, or if I run samples 1+2 or 2+3. The program also ran successfully on all samples when not using paired mode, so I'm confident I'm using the program correctly and that my input files are as they should be.

Could you please advise what would cause the program to error at the pvalue stage? Thank you :)

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yun — Mon, 11 Jul 2022 11:03:25 -0000

why

Home modified by Wei Li

Wei Li — Fri, 25 Mar 2022 03:08:53 -0000

--- v75
+++ v76
@@ -1,6 +1,6 @@
 # Introduction

-#### Note: Try MAGeCK without code on [Latch!](https://latch.bio/) 🧙
+#### Note: Try MAGeCK without code on [Galaxy platform](https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/crispr-screen/tutorial.html) or [Latch!](https://latch.bio/) 🧙

 **Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK)** is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from [Dr. Xiaole Shirley Liu's lab](http://liulab.dfci.harvard.edu/) at Dana-Farber Cancer Institute, and is being actively updated by [Wei Li lab](https://weililab.org) from Children's National Medical Center. The MAGeCK algorithm is described in the following paper:

Home modified by Bicna Song

Bicna Song — Mon, 24 Jan 2022 21:25:53 -0000

--- v74
+++ v75
@@ -1,4 +1,6 @@
 # Introduction
+
+#### Note: Try MAGeCK without code on [Latch!](https://latch.bio/) 🧙

 **Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK)** is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from [Dr. Xiaole Shirley Liu's lab](http://liulab.dfci.harvard.edu/) at Dana-Farber Cancer Institute, and is being actively updated by [Wei Li lab](https://weililab.org) from Children's National Medical Center. The MAGeCK algorithm is described in the following paper:

Home modified by Wei Li

Wei Li — Fri, 09 Oct 2020 18:57:36 -0000

--- v73
+++ v74
@@ -61,6 +61,7 @@
     * Allow mismatches from read mapping
     * Correct copy number variation effect
     * Run MAGeCK on Docker
+    * Make full use of MLE design matrix for more complicated experimental designs (e.g., paired samples, time series) 
     * Include sgRNA efficiency estimation from MLE
 * [Usage](usage)
 * Running MAGeCK as an expert

Home modified by Wei Li

Wei Li — Fri, 09 Oct 2020 16:09:29 -0000

--- v72
+++ v73
@@ -11,7 +11,18 @@
 * [MAGeCKFlute](https://bitbucket.org/liulab/mageckflute/src/master/), an integrative analysis pipeline for pooled CRISPR functional genetic screens.
 * [scMAGeCK](https://bitbucket.org/weililab/scmageck/src/master/), a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data.

+MAGeCK and associated softwares offer a range of functions meet the analys needs of different users, including:

+* Different installation and running options (source code, bioconda or Docker);
+* Simple treatment vs. control analysis (via MAGeCK RRA) and multiple sample comparison analysis (via MAGeCK MLE);
+* Different levels of visualization modules (MAGeCK R markdown, web-based MAGeCK-VISPR, and MAGeCKFlute R package);
+* Starting from either raw fastq files (via MAGeCK count), raw count table, normalized count table (via MAGeCK RRA or MLE), or even sgRNA ranks (via RRA);
+* Various normalization approaches including custom negative control guides/genes;
+* Paired sample analysis (RRA only);
+* Copy-number variation (CNV) correction with or without known CNV profiles of cells;
+* More complicated experimental design including time-series and drug treatment CRISPR screen using MAGeCK MLE;
+
+and so on.

 MAGeCK and MAGeCK-VISPR are free, open source softwares under the BSD license. We greatly appreciate the support from [The Claudia Adams Barr Program in Innovative Basic Cancer Research](http://www.dana-farber.org/How-to-Help/Dana-Farber-Marathon-Challenge/Claudia-Adams-Barr-Program.aspx) and NHGRI (NIH) to develop MAGeCK and MAGeCK-VISPR.

Home modified by Wei Li

Wei Li — Sun, 12 Apr 2020 22:01:57 -0000

--- v71
+++ v72
@@ -25,6 +25,7 @@
 * [Barbieri et al. Nature 2017](https://www.ncbi.nlm.nih.gov/pubmed/29186125), [Reddy et al. Cell 2017](https://www.ncbi.nlm.nih.gov/pubmed/28985567),  [Diao et al. Nature Methods 2017](https://www.ncbi.nlm.nih.gov/pubmed/28417999),  [Michlits et al. Nature Methods 2017](https://www.nature.com/articles/nmeth.4466), [Liao et al. Genes & Dev. 2017](http://genesdev.cshlp.org/content/31/2/184.short)
 * [Sack et al. Cell 2018](https://www.ncbi.nlm.nih.gov/pubmed/29576454), [Bester et al. Cell 2018](https://www.cell.com/cell/abstract/S0092-8674(18)30384-2), [Koren et al. Cell 2018](https://www.sciencedirect.com/science/article/pii/S009286741830521X), [Noordermeer et al. Nature 2018](https://www.nature.com/articles/s41586-018-0340-7), [Shifrut et al. Cell 2018](https://www.sciencedirect.com/science/article/pii/S0092867418313333)
 * [Chen et al. Cell 2019](https://www.ncbi.nlm.nih.gov/pubmed/30735634), [Zhu et al. Cell 2019](https://www.cell.com/cell/pdf/S0092-8674(19)30288-0.pdf), [Lytle et al. Cell 2019](https://www.sciencedirect.com/science/article/pii/S0092867419302727), [Henriksson et al. Cell 2019](https://www.sciencedirect.com/science/article/pii/S0092867418315691), [Behan et. al Nature 2019](https://www.nature.com/articles/s41586-019-1103-9),
+* [Jain et al. Cell 2020](https://www.sciencedirect.com/science/article/pii/S0092867420303214), [Pang et al. Nature Genetics 2020](https://www.nature.com/articles/s41588-020-0578-5), [Crowther et al. Nature Immunology 2020](https://www.nature.com/articles/s41590-019-0578-8?ref=9gag), [Xue et al. Nature 2020](https://www.nature.com/articles/s41586-019-1884-x),

 and so on.

Home modified by Wei Li

Wei Li — Thu, 12 Mar 2020 00:10:47 -0000

--- v70
+++ v71
@@ -5,7 +5,13 @@
 [Li, et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology 15:554 (2014)](http://genomebiology.com/2014/15/12/554/abstract)

-Besides MAGeCK, we also present [MAGeCK-VISPR](https://bitbucket.org/liulab/mageck-vispr), a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens. MAGeCK-VISPR allows you to check the qualities of the screening sample, perform multiple condition comparisons (instead of only two condition comparisons in MAGeCK), and explore the results interactively.
+Besides MAGeCK, we also developed the following softwares and algorithms: 
+
+* [MAGeCK-VISPR](https://bitbucket.org/liulab/mageck-vispr), a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens. 
+* [MAGeCKFlute](https://bitbucket.org/liulab/mageckflute/src/master/), an integrative analysis pipeline for pooled CRISPR functional genetic screens.
+* [scMAGeCK](https://bitbucket.org/weililab/scmageck/src/master/), a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data.
+
+

 MAGeCK and MAGeCK-VISPR are free, open source softwares under the BSD license. We greatly appreciate the support from [The Claudia Adams Barr Program in Innovative Basic Cancer Research](http://www.dana-farber.org/How-to-Help/Dana-Farber-Marathon-Challenge/Claudia-Adams-Barr-Program.aspx) and NHGRI (NIH) to develop MAGeCK and MAGeCK-VISPR.

Home modified by Wei Li

Wei Li — Tue, 04 Feb 2020 21:18:10 -0000

--- v69
+++ v70
@@ -40,9 +40,10 @@
     * [3: Going through a public screening dataset](https://sourceforge.net/p/mageck/wiki/demo/#the-third-demo-going-through-a-public-crisprcas9-screening-dataset)
     * [4: Using MAGeCK MLE](https://sourceforge.net/p/mageck/wiki/demo/#the-fourth-demo-using-mageck-mle-module)
 * [More complicated tutorials](https://sourceforge.net/p/mageck/wiki/demo/#advanced-tutorial)
-    * [Allow mismatches from read mapping](https://sourceforge.net/p/mageck/wiki/demo/#tutorial-1-allow-mismatches-for-read-mapping)
-    * [Correct copy number variation effect](https://sourceforge.net/p/mageck/wiki/demo/#tutorial-2-correct-the-effects-from-copy-number-variations)
-    * [Include sgRNA efficiency estimation from MLE](https://sourceforge.net/p/mageck/wiki/demo/#tutorial-3-include-the-sgrna-efficiency-into-mle-calculation)
+    * Allow mismatches from read mapping
+    * Correct copy number variation effect
+    * Run MAGeCK on Docker
+    * Include sgRNA efficiency estimation from MLE
 * [Usage](usage)
 * Running MAGeCK as an expert
     * [Provide negative control guides](https://sourceforge.net/p/mageck/wiki/QA/#what-does-the-control-sgrna-control_sgrna-option-do-how-to-use-this-option)