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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 information about hard UMI cutoff for filtering #54

Closed allyhawkins closed 2 years ago

allyhawkins commented 2 years ago

Closes #53. Here, I am adding a short note in the filtering section of the processing information to note that if a library does not meet the assumption of emptyDropsCellRanger, that it will be filtered using a hard cutoff instead.

I also added in the additional fields in the metadata filtering_method and umi_cutoff to the sce_file_contents page. I chose to keep everything in the metadata for the sce as one large table, but thought about the idea of breaking out the three pieces of metadata that are only present for the filtered data and include in a small separate table below the first table (similar to how we do the cell metrics section). If reviewers like that idea, I can break out the table, but I wasn't sure if this was completely necessary.

allyhawkins commented 2 years ago

Thanks for taking a look at this and for helping with cleaning up the wording! I incorporated your changes so it's ready for another look.