Combine scRNAseq data for bulk analysis using DESeq2
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evocanres • 0
@evocanres-17914
Last seen 3 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 • 912 views
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ATpoint ★ 4.0k
@atpoint-13662
Last seen 5 hours 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?

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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.

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