Question

Cellranger for BGI scRNAseq sequencing data with "Low Fraction Reads in Cells"?

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2.4 years ago

miao • 0

I have the scRNAseq data sequenced by BGI, which can be processed by cellranger. but the result always show "Low Fraction Reads in Cells" as the fig showed. does anyone know the reason, I also tested my pipeline with 10X test data, result is ok. is there with any mistake I made or some bug between BGI and cellranger enter image description here

scRNAseq BGI cellranger • 1.2k views

ADD COMMENT • link updated 2.4 years ago by GenoMax 141k • written 2.4 years ago by miao • 0

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This indicates a problem with the sample/libraries. Did you start with significantly more cells than recommended by 10x protocol?

ADD REPLY • link 2.4 years ago by GenoMax 141k

score 0 · Answer 1 · 2021-11-19

That is an awfully median # of genes per cell. I just looked at a recent 10X file of my own, and it has a similar overall shape to your image, but the knee bends at about 10k reads, not 1k reads like yours does.

I doubt anything is wrong with the processing; it's probably a problem with the sample prep.