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epi2me-labs / wf-single-cell

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Support for 5' kit version 2? #106

Closed itslittman closed 5 months ago

itslittman commented 5 months ago

Ask away!

Can I use this workflow with data acquired using the 10x Genomics 5' kit version 2? I only see v1 as an option for 5'; that combined with BAM tagging-related errors makes me think that the answer is "no." Assuming I'm on the right track with this thinking, I'm confused why v2 isn't an option despite 10x now being on the v3 kit and with ONT touting version 2 of the 5' kit in single cell-related pamphlets.

Is there a way to at least make some UMAPs with my data?

cjw85 commented 5 months ago

The kit version is used in the workflow only to choose an appropriate whitelist for cell barcodes. This is the same for the V1 and V2 5′ kits, so the workflow should proceed as normal. We will update the documentation of the workflow.

itslittman commented 5 months ago

My bad! I'm not sure why I was getting the errors I was getting but they stopped occurring.