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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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Pooled Prime Editing #207

Closed Cas999 closed 2 years ago

Cas999 commented 2 years ago

Hi @kclem,

Thank you very much for creating and sharing the great tool with the community. Could you instruct me on how to define various parameters for pooled prime editing analysis in Amplicon mode?

In the CRISPRessoPooled instruction, the description file can include up to 5 columns (AMPLICON_NAME, AMPLICON_SEQUENCE, sgRNA_SEQUENCE (OPTIONAL), EXPECTED_AMPLICON_AFTER_HDR (OPTIONAL), CODING_SEQUENCE (OPTIONAL)).

On top of these, I would like to include the following parameters for each amplicon:

--prime_editing_pegRNA_spacer_seq (can be substituted with sgRNA_SEQUENCE (OPTIONAL)) --prime_editing_nicking_guide_seq --prime_editing_pegRNA_extension_seq --prime_editing_pegRNA_scaffold_seq --prime_editing_pegRNA_scaffold_min_match_length --prime_editing_override_prime_edited_ref_seq -qwc

Thank you very much!!

Best,

kclem commented 2 years ago

Thanks @Cas999,

This isn't currently implemented - but we'll see if we can implement it for a future release.

Thanks,

Kendell

Cas999 commented 2 years ago

Hi @kclem,

Thank you very much for your kind consideration! This will help the field a lot!

Best,