Gene-based and transcriptome-based profiling
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5 weeks ago
Chris ▴ 20

Hello bioinformaticians,

-Would you please explain what gene-based profiling means?
-What is the difference between human genome mapping (mapping to Hg38) vs human transcriptome mapping (mapping to transcriptome)?
As I understand transcriptome-based profiling is RNA-Seq analysis.
I asked Google but didn't find the answer.

Thank you so much!

profiling • 445 views
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GenoMax Would you please have some advice?

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Can you clarify as to where your confusion is originating?

Experimentally with RNAseq you are always going to be capturing data from transcribed parts of the genome. You have two options when you analyze this data.

  1. You could align this data to genome and then use an annotation file containing gene models to count the reads that are mapping. Generally people will count reads at exon level but summarize the counts at level of genes, so you end up with one count value per gene. Aligning to genome can help identify parts of the genome that are not known to be transcribed. This approach takes more resources to align to the genome in terms of time/compute power.

  2. Programs like salmon and kallisto take a different approach. They start with a known/de novo transcriptome as a reference. So you are going to be limited to the content of that transcriptome in terms of what you can quantify. Optionally, Salmon can make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads. Aligning to a set of transcripts uses clever statistics that properly accounts for reads that may multi-map (mapping in multiple locations) in the genome. salmon/kallisto approach requires less time and compute resources.

That said both of these approaches are valid and tested.

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Thank you so much for detailed answer! I am not confused about transcriptome-base profiling because I think it is RNA-Seq analysis. I only don't know what gene-based profiling means.

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It may be a case of semantics. When arrays were popular in early 2000s, people used the term "gene-based profiling". Both cases one is looking at gene expression using a different technology.

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May I chat with you somewhere for more detail?

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