What to do if I have both pre-treatment AND WT samples from a CRISPRscreen to analyse
0
0
Entering edit mode
8 weeks ago
chrisgr ▴ 20

I'm trying a crisprscreen analysis using Mageck. I have both pre-treatment(baseline) ánd WT samples (and ofcourse treatment samples). Online I have only found people simply comparing the WT vs treatment. But isn't there a way to include the pre-treatment samples to the command of Mageck in order to normalise the WT and treatment with a baseline first? Or what would be the best approach?

My current command comparing pre-treat vs WT (not including the treatment)

mageck test -k GSE277685_sgRNA_count_table.txt -t Input1_rep1,Input1_rep2 -c WT_week6_rep1,WT_week6_rep2, -n mageck_output/WT/WT_week6

Hope anyone could guide me a bit here

All the best,
Chris

crispr mageck crisprscreen screening • 226 views
ADD COMMENT
0
Entering edit mode

You will want to use mageck mle analysis for that.

ADD REPLY
0
Entering edit mode

Thank you for your response. I'm confused though. Following this: https://sourceforge.net/p/mageck/wiki/demo/#the-fourth-demo-using-mageck-mle-module

From "The fourth tutorial: using MAGeCK mle module" onward, I would not want to compare the HL60 and KBM7 with their initial samples seperately, resulting in 2 P-values (like in the example), What I want is to compare HL60 and KBM7 with eachother and use their initial samples to normalize.

I want 1 P-value that tells me this gene is different between HL60 and KBM7 while normalized based on their initial samples.

I hope I explain my problem well, let me know and thanks again

ADD REPLY

Login before adding your answer.

Traffic: 1167 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6