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Harmony integration of integarted samples

I need to integrate snRNA-seq data from 3 samples (S11, S12, S13) of species1 and 3 samples (S21, S22, S23) of species2. So, I have potential batch effects of library prep among samples of the same species and bio and tech batch effects between different species. Also, when I use harmony for integration, I need to specify group.by.vars which can be 'samples' or 'species'. Which option will be correct:

  1. Run two separate RunHarmony for S21, S22, S23 and S21, S22, S23 and then integrate two resulting objects?
  2. Integrate all samples at the same time. Can I put group.by.vars = c('sample','species') then?

What will be the best way to integrate all samples and remove batch effects associated with sample handling and inter-species heterogeniety?

scrna-seq harmony
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updated by jared.andrews07 jared.andrews07 • written by fifty_fifty • fifty_fifty

1 answer

You have two potential approaches. Just try each and see which seems to work better for your intended purpose. Generally, I just integrate on sample given I'm just trying to cram stuff together to annotate cell types more easily.

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written by jared.andrews07 jared.andrews07

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