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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Update starsolo mapping to accomodate single nuclei #154

Closed jashapiro closed 2 years ago

jashapiro commented 2 years ago

The current version of the STARsolo mapping process at https://github.com/AlexsLemonade/alsf-scpca/blob/main/workflows/genetic-demux/map-sc-star.nf does not properly handle single nucleus data, which we do have for some multiplexed samples.

While I do not think this affects the BAM output, which is the main function we are using, it can affect the quantification, and the UMI/cell counts that are used for identifying and filtering cells. If we want to use STARsolo in the future for quantification, we would want it as well.

This should be a matter of checking the metadata for each sample and adding --soloFeatures GeneFull to include unspliced RNA in quantification.

jashapiro commented 2 years ago

As long as we are adding options, we might want to add --soloMultiMappers EM to use a similar quantification strategy as alevin-fry with EM... adding this adds a new quant matrix, so there is no loss of the original data.

jashapiro commented 2 years ago

closed by #160