Mageck NEST cannot find control genes/sgRNAs
0
0
Entering edit mode
7 days ago
liz.b • 0

When I run mageck nest with the command below, I get the error that the control sgRNAs cannot be found. Does anyone know the correct format to pass the controls to mageck nest?

Command I'm running:

mageck_nest nest -k count.txt \
  -d designmatrix4.txt \
  --norm-method control \
  -e controls.txt \
  -n nest

The only time it can find the controls is if, instead of passing a file for -e, I pass a single gene name:

mageck_nest nest -k count.txt \
  -d designmatrix4.txt \
  --norm-method control \
  -e TERGENIC76054 \
  -n nest

(Which then subsequently throws a long load of python errors, and isn't the analysis I want anyway).

Any format for controls.txt that I can think of doesn't seem to work (and the demo list of controls doesn't work).

Any suggestions appreciated!

python mageck crispr-screen • 196 views
ADD COMMENT
0
Entering edit mode

and the demo list of controls doesn't work

Are you including the names as one per line in the file?

ADD REPLY
0
Entering edit mode

Yes, as far as I can tell.

The demo file looks like:

enter image description here

And my file looks like:

enter image description here

These formats have worked fine with MLE, but don't seem to work with NEST...

ADD REPLY
0
Entering edit mode

For future. Don't post screenshots of text content. You can use 101010 button in the edit window to format text as monospaced code.

ADD REPLY

Login before adding your answer.

Traffic: 3821 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