https://sourceforge.net/p/mageck/wiki/2026-06-12T19:32:51.967000ZRecent changes to wiki2026-06-12T19:32:51.967000Z2026-06-12T19:32:51.967000ZWei Lihttps://sourceforge.net/u/davidliwei/https://sourceforge.netdb34f00042b977ffe8e8062711d8ba09dbceb8b1

<div class="markdown_content"><pre>--- v76 +++ v77 @@ -1,4 +1,5 @@ # Introduction +#### Note: MAGeCK2 is the next generation of MAGeCK. Check it out [here](https://github.com/davidliwei/mageck2). #### 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/) 🧙 </pre> </div>

2025-09-16T20:00:15.326000Z2025-09-16T20:00:15.326000Zlovisha aggarwalhttps://sourceforge.net/u/lovisha20/https://sourceforge.netcb45934934bc6008ed05312974df93f0d3817fa6

<div class="markdown_content"><p>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?</p></div>

2023-10-16T20:11:19.185000Z2023-10-16T20:11:19.185000ZWei Lihttps://sourceforge.net/u/davidliwei/https://sourceforge.neted1bc4e76e7814a20502effd5f52d74d300d0072

<div class="markdown_content"><pre>--- v54 +++ v55 @@ -196,7 +196,7 @@ For simplicity, let's assume you already know how to generate read count table from fastq files; if not, check [the third demo](https://sourceforge.net/p/mageck/wiki/demo/#the-third-demo-going-through-a-public-crisprcas9-screening-dataset) above. We will use the read count table presented in [T Wang et al. Science 2014](http://www.ncbi.nlm.nih.gov/pubmed/24336569). -Download the read count table [here](http://https://sourceforge.net/projects/mageck/files/example/leukemia.new.csv/download). +Download the read count table [here](https://sourceforge.net/projects/mageck/files/example/leukemia.new.csv/download). ### Step 2: prepare the design matrix file ### </pre> </div>

2023-09-11T20:24:01.354000Z2023-09-11T20:24:01.354000ZWei Lihttps://sourceforge.net/u/davidliwei/https://sourceforge.net423388aeff488b3df49445e752009edee0a925c2

<div class="markdown_content"><pre>--- v69 +++ v70 @@ -7,14 +7,14 @@ To install MAGeCK through bioconda channel, first download and install the Python 3 variant of the [Miniconda Python distribution](http://conda.pydata.org/miniconda.html). Then, in the command line, type ::bash - conda install -c bioconda mageck + conda install -c bioconda -c conda-forge mageck That's it! An optional step (but recommended) is, you can create an isolated software environment for mageck by executing ::bash - conda create -c bioconda -n mageckenv mageck + conda create -c bioconda -c conda-forge -n mageckenv mageck in a terminal. The environment can be activated via </pre> </div>

2023-09-11T15:32:37.380000Z2023-09-11T15:32:37.380000ZPasqualehttps://sourceforge.net/u/pastoma/https://sourceforge.netf794a717f5ba1273be0601c03c9bdc48eca638fc

<div class="markdown_content"><p>Dear<br/> I have a matter to submit. I'm trying to do a paired analysis, however, I'm getting this error. <br/> <strong>Error: incorrect number of dimensions in line 2 (16) compared with the header line (4). Please double-check your read count table file.</strong><br/> This is the header of my count matrix and it doesn't seem to have apparently problem</p> <p>$ head COUNTS_paired_sor_T0.count.txt<br/> sgRNA Gene SOR_r1 SOR_r1 SOR_r1 SOR_r2 SOR_r2 SOR_r2 SOR_r2 T0_r1 T0_r1 T0_r1 T0_r2 T0_r2 T0_r2 T0_r2 T0_r2 T0_r2<br/> Pgd_sg155_1 Pgd 2989 995 1685 908 1127 1264 1196 1110 666 413 959 1391 1357 1235 1375 1366<br/> Smn1_sg208_4 Smn1 4792 1854 2605 1333 1772 2158 2242 2046 1201 710 1577 2433 2574 2037 2010 2033<br/> Cyp27a1_sg044_3 Cyp27a1 3210 1307 1746 885 713 562 642 660 671 362 819 1281 770 647 616 673<br/> Gca_sg079_3 Gca 4815 1544 2527 1571 869 810 866 880 860 533 1240 1895 1218 748 1046 831<br/> Gstk1_sg087_5 Gstk1 2998 1130 1819 1037 2214 2459 2508 2431 849 443 1029 1724 3030 2230 2501 2508<br/> Ddo_sg048_3 Ddo 2765 1176 1780 911 863 787 885 884 628 313 793 1511 1250 834 910 894<br/> Ehhadh_sg057_3 Ehhadh 5063 1674 3002 1512 2347 2594 2740 2944 1091 680 1533 3007 2856 2361 2621 2293<br/> Mapk1_sg117_2 Mapk1 5369 2006 3483 1893 877 1216 934 1069 1273 709 1522 2837 1654 1260 1305 1267<br/> Rbm6_sg183_6 Rbm6 7618 2926 4661 2568 2136 2332 2215 2283 1434 790 1914 3226 2617 2044 2337 2007<br/> the commands I used are the following:<br/> mageck test -k COUNTS_paired_sor_T0.count.txt -t SOR_r1 SOR_r1 SOR_r1 SOR_r1 SOR_r2 SOR_r2 SOR_r2 SOR_r2 -c T0_r1 T0_r1 T0_r1 T0_r1 T0_r2 T0_r2 T0_r2 T0_r2 -n sor_T0_paired --paired</p> <p>Can anyone suggest a solution?<br/> thank you</p></div>

2022-10-06T12:16:59.465000Z2022-10-06T12:16:59.465000ZMiChttps://sourceforge.net/u/albero/https://sourceforge.net5e9298088e8138ad1df022906f4294fa6601c77a

<div class="markdown_content"><p>I noticed problem with using CNV normalization. For example CNV data for HT1080 cell line form Q4 21 (depmap) works but most recent 22Q2 doesn't and there is error message:</p> <p>INFO @ Thu, 06 Oct 2022 11:57:08: Performing copy number normalization ...<br/> Traceback (most recent call last):<br/> File "/usr/local/bin/mageck", line 66, in &lt;module&gt;<br/> main();<br/> File "/usr/local/bin/mageck", line 43, in main<br/> args=crisprseq_parseargs();<br/> File "/usr/local/lib/python3.10/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs<br/> mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command<br/> File "/usr/local/lib/python3.10/site-packages/mageck/mlemageck.py", line 225, in mageckmle_main<br/> betascore_piecewisenorm(allgenedict,CN_celllabel,CN_arr,CN_celldict,CN_genedict,selectGenes=genes2correct)<br/> File "/usr/local/lib/python3.10/site-packages/mageck/cnv_normalization.py", line 125, in betascore_piecewisenorm<br/> opt_bp = optimize.minimize(leastsq_bp,2,bounds=((1,np.percentile(CN_vals,99.9)),))<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_minimize.py", line 699, in minimize<br/> res = _minimize_lbfgsb(fun, x0, args, jac, bounds,<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_lbfgsb_py.py", line 362, in _minimize_lbfgsb<br/> f, g = func_and_grad(x)<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py", line 285, in fun_and_grad<br/> self._update_fun()<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py", line 251, in _update_fun<br/> self._update_fun_impl()<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py", line 155, in update_fun<br/> self.f = fun_wrapped(self.x)<br/> File "/usr/local/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py", line 137, in fun_wrapped<br/> fx = fun(np.copy(x), *args)<br/> File "/usr/local/lib/python3.10/site-packages/mageck/cnv_normalization.py", line 115, in leastsq_bp<br/> (slope,intercept) = linreg_bp(bp)<br/> File "/usr/local/lib/python3.10/site-packages/mageck/cnv_normalization.py", line 110, in linreg_bp<br/> stats.linregress(CN_vals<span>[CN_vals&lt;=bp]</span>,score_vals<span>[CN_vals&lt;=bp]</span>)<br/> File "/usr/local/lib/python3.10/site-packages/scipy/stats/_stats_mstats_common.py", line 153, in linregress<br/> raise ValueError("Inputs must not be empty.")&lt;/module&gt;</p> <div class="codehilite"><pre><span></span><code><span class="nv">I</span><span class="s1">'</span><span class="s">m using function to prepare file for CNV normalization so format of this file is exactly the same. Difference is only in cn numbers....</span> </code></pre></div> <p>Anyone has idea what is going on?</p> <div class="codehilite"><pre><span></span><code>Thanks MC </code></pre></div> </div>

2022-08-24T23:52:16.029000Z2022-08-24T23:52:16.029000ZFiona Hartleyhttps://sourceforge.net/u/fionamh/https://sourceforge.netcad2a780ba6aa0ecd0ebd2ee89a66ac74305c63a

<div class="markdown_content"><p>Hello, <br/> I'm getting the following error message when running mageck test in --paired mode<br/> "An error occurs while trying to compute p values. Quit.."<br/> Up until then, the log file appears normal.</p> <p>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.</p> <p>Could you please advise what would cause the program to error at the pvalue stage? Thank you :)</p></div>

2022-07-11T11:03:25.467000Z2022-07-11T11:03:25.467000Zyunhttps://sourceforge.net/u/yunzhang/https://sourceforge.net2b83defe1c8c1bf89209e4fb895049f4ccdc10e3

<div class="markdown_content"><p>why</p></div>

2022-04-30T02:13:13.483000Z2022-04-30T02:13:13.483000ZWei Lihttps://sourceforge.net/u/davidliwei/https://sourceforge.net7371ce946bc9af859efefeec3625bf5b1eeceb21

<div class="markdown_content"><pre>--- v23 +++ v24 @@ -50,7 +50,7 @@ * The element in the design matrix is either "0" or "1". * You must have at least one sample of "initial state" (e.g., day 0 or plasmid) that has only one "1" in the corresponding row. That only "1" must be in the baseline column. - +*Note:* different orders of the samples in the design matrix may change the results, because there are preprocessing steps to remove outliers. A good practice will be to always place initial samples (like day0 or plasmid) as the first rows in the design matrix. ## sgRNA library file ## </pre> </div>

2022-03-25T03:08:53.921000Z2022-03-25T03:08:53.921000ZWei Lihttps://sourceforge.net/u/davidliwei/https://sourceforge.neteda9ed1237c9e3fe4ee3f447df924834f0c00cf9

<div class="markdown_content"><pre>--- 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: </pre> </div>