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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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Cannot run Crispresso2 with more then one pegRNA, pegRNA_extension and ngRNA #232

Open JH1606-code opened 2 years ago

JH1606-code commented 2 years ago

Hi all,

I did an PE screen where I have more than one edit induced in the same sequence. So this means I have one amplicon as reference but more than one pegRNA, pegRNA extension sequences and ngRNAs. I expected to run CRISPResso2 by separating the sequences of the single pegRNAs, ngRNAs and pegRNAs extension with commas.

But I always end up with the following error:

ERROR: The prime editing pegRNA spacer sgRNA sequence contains bad characters:,

The script run through when I use always one sequence, but as soon I add further pegRNA, ngRNA or pegRNA extension sequences (separated by comma) I get the error. So it seems that it's not possible to run CRISPResso 2 with more than one sgRNA sequences?

I would be happy about a feedback!

Best wishes

Colelyman commented 2 years ago

Hi @JH1606-code,

Thanks for using CRISPResso2. As you have discovered we currently don't support multiple pegRNA, pegRNA extension sequences or ngRNAs. However, this is on our roadmap to implement. You can have multiple sgRNAs, but the PE specific parameters only support one sequence.

Sorry for the trouble!