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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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Begin addition of Alevin-fry processing information for single-nuclei and single-cell samples #3

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

This PR adds some initial processing information for alevin-fry and is stacked on #2. I began with one markdown file processing_information.mdand filled out the headers to outline the information that I was thinking should be included in that document. I then used make html to build the _build/html/index.html file that can be viewed and contains the generated links to view the markdowns. The only files I directly edited myself were processing_information.md and index.rst.

For the actual documentation, I broke it up into two main sections, processing of single-cell and single-nuclei samples and processing of bulk RNA samples. Within the single-cell and single-nuclei samples I am thinking we can include sub sections about if a sample has an associated CITE-seq or spatial library.

For the section covering single-cell and single-nuclei samples, I chose to include an overview of the alevin-fry pipeline we are using followed by three sections covering index choice, alignment choice, and then count collapsing for single cell vs. single nuclei.

Here I am hoping for some general overview comments to help us get started building the rest of the documentation, in particular:

  1. Does this organization make sense or do reviewers have other ideas for ways to organize these topics? Should we maybe split up this file more?

  2. I also chose to include a few short sentences of why we chose Alevin-fry over cellranger. I wasn't sure at what level of detail we should be covering this topic, if at all?

  3. I did not include any information about actually running the nextflow pipeline yet. I am thinking that will be a different section, do others agree or would we rather integrate that information into this text?

allyhawkins commented 3 years ago

@jaclyn-taroni Thanks for the feedback! I went ahead and removed the intro paragraph and moved the section that talked about the alevin-fry options like --unfiltered-pl to it's own section after the discussion of the index and alignment like you suggested.

I also did some restructuring of the splici discussion including removing the section on actually generating the index. I tried to keep the discussion on the simpler side only including the points that I thought were relevant to understand what was actually done, but let me know if that is not the correct level of detail and if there are more or less concepts that should be included? I also think there may be points here where we would want to link to code or notebooks with more detailed information, like generating the splici index (but that would be for another PR).

allyhawkins commented 3 years ago

Thanks for the feedback, @jashapiro. Based on your comments, I went ahead and made the decision to change everything to be in sentence case so it should be consistent. Also for use of alevin-fry and salmon in the text, I chose to use code formatting. If others feel strongly against this and would prefer a different format, I'm happy to change it.

I also went through and cleaned up some of the areas that you had pointed out like the description of the splici index and the resolution description within the Alevin-fry parameters section.