Use the single cell RNA-seq data for normal transcriptome analysis

Question

[fanglujing]

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.

[GouthamAtla]

What you want to do with the data ?

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

What analysis ?

[fanglujing]

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

[Friederike]

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

[fanglujing]

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.

Answer 1

[GouthamAtla]

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.

[fanglujing]

hey, geek_y, thanks for your helpful reply.