snRNASeq: How to fix low fraction reads in cells and high fraction map to antisense gene warnings?

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22 months ago

Claire • 0

Hi Every one

I use cell ranger v6 to analyse single nuclei rnaseq, so I set include-introns to true. I got the warnings in the image of low fraction of reads in cells and high fraction map to antisense genes. My question is:

How to find if I have ambient RNA
How to decide what number to use in force-cell, how to investigate the data for this?
If I am using the Single Cell 3' v3 chemistry and it seems correct, how to check? Thanks a lot

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cellranger snRNASeq • 1.2k views

ADD COMMENT • link 22 months ago by Claire • 0

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What type of sample is this, and how was the cell viability going into it?

ADD REPLY • link 22 months ago by rpolicastro 13k

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Thank you. This is human single nuclei single cellRNAseq data. I don't know the cell viability, not sure. Thanks

ADD REPLY • link 22 months ago by Claire • 0

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