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| | `af_resolution` | `alevin-fry quant` resolution mode used | | ||
| | `usa_mode` | Boolean indicating whether quantification was done using `alevin-fry` USA mode | | ||
| | `af_num_cells` | Number of cells reported by `alevin-fry` | | ||
| | `mapping_tool` | Pipeline used for mapping and quantification. `alevin-fry` for all tag-based experiments (e.g. 10Xv2, 10Xv3) and `cellranger-multi` for probe-based experiments (GEM-X Flex) | |
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I can neither confirm nor deny that I just spent 3 minutes being really confused why we don't set this for spaceranger too, only to remember we do not make SPEs. That's the other thing I work on (training materials).
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| ### Mapping and quantification for GEM-X Flex samples | ||
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| Libraries that were generated using the GEM-X Flex technology from 10x Genomics were quantified with the [`cellranger multi` pipeline](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-multi) within Cell Ranger. |
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Comment that applies throughout PR - pick either cellranger multi or cellranger-multi
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So that's intentional. We use cellranger-multi as the mapping tool in the object. But the function is noted as cellranger multi on the 10x site. It was kind of bothering me when I was writing this, so I think that's a sign to just change this line in scpca-nf to have the space. https://github.com/AlexsLemonade/scpca-nf/blob/80e7bbb78202ba6cb618feab59af433c750fcdc7/bin/generate_unfiltered_sce_cellranger.R#L164
Co-authored-by: Stephanie J. Spielman <stephanie.spielman@gmail.com>
…g-faq Restore FAQ for downloading programmatically
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Okay I filed AlexsLemonade/scpca-nf#1234 and now use |
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Closes #491
This PR adds in documentation for the 10x flex libraries that are going to be on the Portal soon. I updated the processing information page to include a section on using
cellranger multifor GEM-X Flex libraries. To do this I rearranged some of the existingalevin-frycontent slightly. Mostly, I wanted to talk about everything specific toalevin-fryall the way through reading in the counts data in one section and then the Flex stuff in a different section. Everything after that is the same regardless of technology.I also updated the metadata slots in the individual SCEs and merged SCEs to add the new cellranger specific slots (see https://github.com/AlexsLemonade/scpca-nf/blob/fa640c3c86de99a7190264949646e392ed9ecdbb/references/sce-formatting-reference.json#L66-L70). I also denoted which ones were only present if mapping was done with
alevin-fry. Lastly, I rearranged the order slightly to group all the alevin-fry specific ones and cellranger multi specific ones together.