Filter step: Background file

[jsacco1]

In my experiment, I have a control that does not have a background file. My understanding is that one is supposed to have a sample that was just transfected with the oligo tag without Cas9 as background control, but we do not have that sample. What do I put for the background file in this case?

Also can guideseq handle PAMs that are not NGG, as we have a different Cas9 that uses NNGRRT? If so, where can that be modified/accounted for?

[YichaoOU]

Hello,

You can just use some fake barcode sequences and start the analysis. Let me know if it doesn't work.

    control:
        target:
        barcode1: AAAAAAAA
        barcode2: AAAAAAAA
        description: Control

You can specify the PAM sequence by PAM: NNGRRT in the yaml file.

Yichao