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Error while running pipeline with 10x -3 prime v4 kit #108

Closed Bioinfo9 closed 5 months ago

Bioinfo9 commented 5 months ago

Ask away!

Hi ! I have been using the epi2me sc pipeline with 10x -3prime v3 kit with the parameter, expected no of cells :500. We have now updated the kit to 10x- 3prime v4 . In this the expected no of cells is 15000. But I’m not able to execute the pipeline in the end it shows error where all genes are getting filtered . What could be the possible issue . Thank you

nrhorner commented 5 months ago

Hi Bioinfo9

It appears that the 10x v4 kit utilizes a different whitelist to v3 https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist

This may be the cause of your issues. I'll look at getting V4 supported as soon as possible.

bioinfo23 commented 5 months ago

Thank you for your response.