single nucleus RNA seq processing pipeline questions

Question

[biotrekker]

Hello, I am working with a snRNA-seq dataset. The individuals are pooled into multiple batches and the only way I know whos who is because the dataset maps cell barcodes to individual id. How should I go about processing this data? When should I "demultiplex" and how? Can I trim and align first, and then "demultiplex"?

By demultiplex I mean the process of separating out multiple samples pooled into a single library, which is different from demultiplexing in sequencing.

Thanks

[dsull]

1. What software are you using (CellRanger, kallisto, alevin, or STARsolo)?

2. I'll need more information about the file structure. Do you mean there are no barcodes (e.g. you have 800 cells, and you therefore have file1.fastq.gz, file2.fastq.gz, ..., file800.fastq.gz)? Do you mean that there are barcodes but, say we have a barcode ATGGCA, ATGGCA in file1.fastq.gz is a different cell than ATGGCA in file2.fastq.gz?

[biotrekker]

Thanks this worked!