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welch-lab / MultiVelo

Multi-omic velocity inference
BSD 3-Clause "New" or "Revised" License
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Multi-omic #25

Open zhangqc723 opened 1 year ago

zhangqc723 commented 1 year ago

Hello, Now, I had got the output form 10X Multi-omic (RNA+ATAC) by cellranger-arc, and I want to use velocyto run10x for my RNA data form 10X RNA+ATAC. What should I do? Thanks

danielee0707 commented 1 year ago

Please follow Velocyto's documentation to run their CLI tool. See http://velocyto.org/velocyto.py/tutorial/cli.html#run10x-run-on-10x-chromium-samples.

If that doesn't work on Multiome, you can also try directly calling Velocyto run http://velocyto.org/velocyto.py/tutorial/cli.html#run-run-on-any-technique-advanced-use using the 10X barcode file for --bcfile argument and gex_possorted_bam.bam as the input BAM file.