Use the single cell RNA-seq data for normal transcriptome analysis
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2.1 years ago
fanglujing ▴ 60

Hi, there I wonder if it is possible to use single cell RNA-seq data as the normal transcriptome data. I want to use CHO-K1 cell RNA-seq data for analysis, and I found a set of data(PRJDB6793) which belong to single cell data. There are 2 types of cells including G0/G1 phase and G2/M in this project. So, what should I do? Combine all the data? Any useful suggestions would be appreciated.

RNA-Seq single cell • 559 views
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What you want to do with the data ?

I want to use CHO-K1 cell RNA-seq data for analysis

What analysis ?

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well, like gene expression, finding novel transcripts, SNP calling, difference analysis (compare with other RNA-seq data), KEGG and GO analysis etc.

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What is the underlying biological question you want to address? Why not look for bulk RNA-seq data?

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I also collected RNA-seq data too. I want to collect these kinds of data as many as possible. So, now I know what should I do with the single-cell RNA-seq data since geek_y shed me some light. Thanks for your reply.

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2.1 years ago

Gene expression, finding novel transcripts (very less likely unless you have full length transript data for 1000s of cells) should be fine but differential analysis comparing to bulk rna-seq does not work because there are many confounding factors like technology,platforms,batches etc etc.

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hey, geek_y, thanks for your helpful reply.

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