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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Add filtering information to processing docs #20

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

Closes #18. In this PR, I'm adding in the section about how we created the filtered counts matrix post processing with Alevin-fry. I added in a brief paragraph about using DropletUtils::emptyDrops() including a sentence about what it does, our choice of lower=200, and then how we actually filtered on the FDR <= 0.01. Please let me know if the explanation is at the right level of detail or not.

Another thing I wanted to note here is that we haven't yet mentioned the actual file types that we are working with or that we have both an unfiltered and filtered output. I was wondering if we should include that here somewhere or have a separate section describing what files are included for each sample (Maybe this is a good candidate for a FAQ)?

Also in this PR I removed the headers for bulk RNA seq and spatial since that will not be part of MVP I thought it made sense to remove for now and then we can add it in when we set up the workflow for those.

jaclyn-taroni commented 3 years ago

Another thing I wanted to note here is that we haven't yet mentioned the actual file types that we are working with or that we have both an unfiltered and filtered output. I was wondering if we should include that here somewhere or have a separate section describing what files are included for each sample (Maybe this is a good candidate for a FAQ)?

This is tracked in #6 so if you have thoughts after writing this, you can jot them down there!

Edit: at least I think that is what you meant

allyhawkins commented 3 years ago

@jashapiro I changed the intro section to combine what I had with what you had suggested. Let me know what you think!