The Difference Between Genome Reference(scRNAseq) And Transcriptome Reference(bulk RNAseq)

Question

[diqixiaoyaoer]

I want to know the difference between Genome Reference in scRNAseq and transcriptome reference in bulk RNAseq.

But I didn't get any better answer in any other place.

I know we could download genome reference from UCSC, NCBI, ENSEMBL and GENECODE for bulk RNAseq. And here are the links below:

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GENCONDE GENCONDE2

UCSC

ENSEMB

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Also ,I find the genome reference links for scRNAseq in Illumina(a link summary page):

Illumina We can download these resource for scRNA sequencing.

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Besides, 10x provides us its own link for scRNA seq: https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest

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However, I don't know the exact difference between genome reference in scRNAseq and transcriptome reference in bulk RNAseq except the file size.

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And, I have read the question here:What Is The Difference Between Genome Reference And Transcriptome Reference? and @Chris Miller answered its question. He said : Transcriptome references generally consist of only the coding regions of the genome. This may include genes with all of their introns spliced out, as well as all known transcripts of a gene, including alternate starts or splice junctions, exon skipping, etc.

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My QUESTION is if I can use the same genome reference and gene annotation files ? For example, could I only use the genome reference and gene annotation files downloaded from UCSC in scRNAseq ?

Or I should distinct them by scRNAseq and bulk RNA seq ?

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[diqixiaoyaoer]

Any body can help me ?

Answer 1

[swbarnes2]

If you want to keep things simple, you could use 10XGenomics references, which will include STAR genomic index. You could use that for bulk RNASeq. Just make sure you understand what reference version it is, and take a glance at the 10XGenomics page to see what gene filters were applied. I think those filterings are perfectly reasonable. but you should still know what they are. Also note that currently, 10XGenomics uses a rather old version of STAR to make its indices, so you might not be able to use the very newest version of STAR on those indices.