Hi all. I’d like to ask about a possible thesis contribution to nf-core/scrnaseq around 10x CITE-seq via cellranger multi. Is #CHN5BV5DW the right place for that discussion? Where can I propose such an addition?

Is the current pipeline unable to do CITE-seq?

Hey, cool to see another person from the Munich ecosystem here. For CITE-seq, it should be supported via cellranger multi, at least that's what I get from this issue. I tried summarizing supported protocols as good as possible here, but I think I wrote this before cellranger multi was supported, or I forgot about it Could you try process your data with the existing implementation and let us know if you encounter any issues? Then we can discuss how we can adapt the pipeline/documentation to make this process easier to understand for future users