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Running on a bam file and cell barcode annotation #25

Open sangho1130 opened 4 months ago

sangho1130 commented 4 months ago

Hi, I'm trying to run SPLASH on my single cell data, and is it possible to run SPLASH by feeding a bam file with barcode-cell type annotation? I'm currently extracting read names from my bam file and separating raw fastq (would result in thousands of files..). I'm wondering if there is a smart way to run this case!

marekkokot commented 4 months ago

Hi,

We are working on a 10X/Visium version of SPLASH, but it's not public-ready yet. For now, it works only for fastq files, but I think bams may be converted with https://www.10xgenomics.com/support/software/cell-ranger/latest/miscellaneous/cr-bamtofastq

Anyway, I'm afraid it will probably take us some time yet to finish and publish 10X/Visium support.

sangho1130 commented 4 months ago

Thank you!