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welch-lab / MultiVelo

Multi-omic velocity inference
BSD 3-Clause "New" or "Revised" License
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MultiVelo for multipo samples #17

Open Lei-Guo opened 1 year ago

Lei-Guo commented 1 year ago

Hi,

Thanks for the awesome package. I've got some questions.

  1. How do I use MultiVelo on multiple samples? The demo seems to be for 1 sample only.

  2. The peaks in my scATACseq dataset were called using MACS2. How do I deal with the "feature_linkage.bedpe" files? Should I make my own linkage file using "LinkPeaks"?

danielee0707 commented 1 year ago

Hi, thank you for using the package. To use multiple samples, one needs to first remove batch effects if there are any. The procedure can be a little complicated, and I wrote the steps we took in discussion #10. I think LinkPeaks should be able to output an object that describes peak-gene correlations. I have never used this function before, but you may need to manually change the format of the output to mimic the structure of a bedpe file from 10X. Either CellRanger ARC V1 or V2 would work. See https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/analysis#fl_output for column descriptions. Alternatively, you can start a test run by using an empty bedpe file, so only promoters are considered.