Cutsite / Linearization Efficiency - How?

[VBHerrenC]

Hello,

I am running wf-clone-validation v1.7.1 locally. I am wondering how to get the linearization efficiency to be part of the report as it mentions in the Pipeline Overview (step 13)? I have run it with a sample and a plasmid reference, and added a "cut_site" column to my sample sheet but there are no stats generated in the report. Is there something else I need to add? How can I get the report to generate this stat? Thanks!

[sarahjeeeze]

hi! We will aim to improve the documentation around this. are you providing full_reference parameter and check https://github.com/epi2me-labs/wf-clone-validation/blob/master/test_data/sample_sheet_cutsite.csv you're sample sheet matches the format here? If you could share your input cmd it might help me determine why its not running?

[VBHerrenC]

Hi @sarahjeeeze,

Thanks for the response! I am running it on the Epi2Me app but can run it on the command line if that would be helpful for you. My sample sheet matches the example exactly and I am providing a full plasmid reference. Should these results be generated with the test data? If so, when I run the test data it is not generated either. I can provide the nextflow execution logs if that would be helpful. Is there a minimum length the cutsite needs to be? I provided strictly the recognition site for my restriction enzyme but in the sample sheet they look a bit longer than that. Thanks!

Calleigh