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aryeelab / guideseq

Analysis pipeline for the GUIDE-seq assay.
GNU Affero General Public License v3.0
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Filter step: Background file #63

Open jsacco1 opened 3 years ago

jsacco1 commented 3 years ago

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 commented 3 years ago

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