Running on a bam file and cell barcode annotation

[sangho1130]

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]

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]

Thank you!