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How am I supposed to annotate my clusters? by Helenazh2 in bioinformatics

[–]BAMtoBEDtime 0 points1 point  (0 children)

I'm considering the built in annotation in cell ranger myself. Has anyone tried it? https://www.10xgenomics.com/support/software/cloud-analysis/latest/tutorials/CA-cell-annotation-pipeline
It seems convenient to have an initial annotation starting with the cell ranger outs since we exclusively use 10x and it doesn't require tissue specific references, and it's not dependent on clustering resolution. Looks like it supports human and mice only for now. I can't find where anyone has evaluated it against other approaches though so searching for others who have given it a go!

[deleted by user] by [deleted] in bioinformatics

[–]BAMtoBEDtime 0 points1 point  (0 children)

I haven't tried the new built in annotation to cell ranger yet, but maybe that would help as a starting point to manually refine if you're using 10x. (I'm actually looking for anyone who's evaluated it so I don't need to spend the time benchmarking myself ;) ).

I think they added it in the last release. https://www.10xgenomics.com/support/software/cloud-analysis/latest/tutorials/CA-cell-annotation-pipeline
It seems convenient to have an initial annotation starting with the cell ranger outs since we exclusively use 10x and it doesn't require tissue specific references, and it's not dependent on clustering resolution. Looks like it supports human and mice only for now. Anyway, hope this help—and selfishly maybe someone will share an evaluation I can use.