Methods for processing CITE seq and HTO data #52
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sjspielman
approved these changes
Feb 28, 2024
Co-authored-by: Stephanie Spielman <[email protected]>
jashapiro
approved these changes
Feb 28, 2024
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| Bulk RNA-seq reads for each sample were mapped to a reference genome using `STAR` [@doi10.1093/bioinformatics/bts635] and multiplexed single-cell or single-nuclei RNA-seq reads were mapped to the same reference genome using `STARsolo`[@doi:10.1101/2021.05.05.442755]. | ||
| The mapped bulk reads were used to call variants and assign genotypes with `bcftools mpileup`[@doi:10.1093/gigascience/giab008]. | ||
| `cellsnp-lite` was then used to genotype single-cell data at the identified sites found in the bulk RNA-seq data [@doi:10.1093/bioinformatics/btab358]. |
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I don't know if we want through throw in a reference to "mode 1a" here, but I had that in the last paper that talked about this. I think it is fine without it.
Co-authored-by: Joshua Shapiro <[email protected]>
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February 28, 2024 21:11
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Click the link below to download the manuscript build as a ZIP file. |
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Closes #39
Closes #40
Stacked on #38
This PR fills in the methods for processing ADT and HTO data. The first section covers quantification of both of these data types. The next sections include information on processing ADT and then demultiplexing. Is the level of detail okay? Are there things that we think are important that are missing?
I'm going to tag in both @jashapiro and @sjspielman, so that @jashapiro can look at HTO and @sjspielman can look at ADT items.