Question

Combine scRNAseq data for bulk analysis using DESeq2

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evocanres • 0

@evocanres-17914

Last seen 13 months ago

United States

I have scRNAseq data from Fluidigm C1 platform, but I have low number of cells (sample 1 ~30, sample 2 ~ 20). Can I merge the fastq files for each samples and treat them bulk RNAseq data to use in DESeq2.

The Fluidigm C1 does full length transcript sequencing, so I am assuming this should be okay? Any thoughts ?

Thank you

DESeq2 scRNAseq Fluidigm • 1.2k views

ADD COMMENT • link 2.3 years ago • updated 2.2 years ago evocanres • 0

score 1 · Answer 1 · 2022-10-10

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ATpoint ★ 4.6k

@atpoint-13662

Last seen 4 days ago

Germany

Pseudobulk aggregation and DESeq2 is basically compatible, it would be 2 samples though and 1vs1 is not supported (or meaningful). With that few cells it raises the question whether the experiment failed and you should even use the data, no?

ADD COMMENT • link 2.3 years ago ATpoint ★ 4.6k

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You would normally get not many cells in Fluidigm C1 Chip. I have seen publications with fewer cells. In contrast to the 10x genomics where there are tens of thousands, 1 C1 chip can only have 96 wells.

ADD REPLY • link 2.2 years ago evocanres • 0