allyhawkins
commented
2 years ago Just noting here that I pulled out the download section into its own PR (#82) and have updated this accordingly. I also added in one link between the processing and sce file contents from my previous review comment. I believe this should be ready to go but will leave the final call up to @jashapiro.
jashapiro
This PR adds docs to describe the processing and file contents for multiplexed libraries.
I struggled a lot to decide what the level of detail should be, so I welcome any thoughts about where there should be more or less detail. For example, I only described the "final" calls for the various demultiplexing programs, and left the (many) individual statistics descriptions as an "exercise to the reader". Let me know if you think I shoudl take a different approach there.
I also tried to update the description of the folder structure and library/sample relationships... I don't love anything that I wrote, but I think it gets the idea across? Let me know if you have improvements.
The folder naming may be in flux, I suppose. I currently say that multiple samples are comma separated, as that is the current output structure, but that seems like it could still change when building the download files.
I also think we decided that that library metadata file would have multiple lines per library, so I didn't think there was any need to change the description of that table.
I made a couple other changes, like including the folder images in the repo. I think this will should (it does for local builds), but if there is some reason those were not included before, please let me know!
Closes #64, but I am leaving it as a draft for now.