negative control sgRNA list error

[Qingcai Meng]

Hi

when I ran Megake mle function from the demo(PAGE 769 of NP paper), it showed several time this error “ Gene ITIH6 consists of both negative controls (2) and non-negative controls (2). This is not allowed -- please check your negative control sgRNA list. “ When i delete this gene, many other genes have been showed with error too, any suggestion?

‌

Thanks,

QM

[Wubing Zhang]

Hi,

From the error message, I suspect you didn’t include all sgRNAs targeting the negative control genes in the negative control sgRNA list. So could you regenerate your negative control sgRNA list and retry?

Best

[Qingcai Meng]

Hi Wubing,

Thanks for your reply. The list was from your paper demo, I just try to run and learn this method (beginner for data analysis). I used your demo files (designmatrix.txt, nonessential_ctrl_sgrna_list.txt, rawcount.txt) under the folder of ‘’mageck_mle”, from the zip file “demo.tar.gz”http://cistrome.org/MAGeCKFlute/, these files are kindly provided by you. Could you run it from your side to see whether you also have this error come up?

Thanks.

(Btw, I use this code to activate Mageck and run follow your papers’ code in a mac terminal:

1. conda activate mageckenv
2. mageck mle --count-table rawcount.txt --design-matrix designmatrix.txt --norm-method control --control-sgrna nonessential_ctrl_sgrna_list.txt --output-prefix braf.mle)

‌

best,

Qingcai