RNA-Seq Mapping Genome or Transcriptome

Question

[santos48]

Hope all you are well, I was confused about thinking Rna Sequencing Mapping with Gene or Transcriptome. Which should I choose for Rna-Seq Analysis, I know it's changing for the goal, but which one should I choose for which goal. Thank you for your comments

[ponganta]

It depends on your goals and organism. RNA-Seq is too broad of a field to provide a simple answer as tried by the commenter below. Especially transcripome-based analyses have made a huge leap forward recently, as e.g. de novo transcriptomics gets more and more reliable.

Answer 1

[Tm]

You should use reference genome for RNASeq mapping as it is complete representation of all genes present in particular organism. When you use transcriprome as reference it represents only the set of genes which were expressed at particular time or condition when RNA was collected. So when you map your data on it you might miss information of genes which are expressed in your sample but not present in transcriptome you are using as reference.

Answer 2

[bigomics.team]

Do you mean gene level Vs transcript level mapping? If you don't care about splice variants, gene level is ok. Mostly people use gene level. I would say, do gene level first and if you don't find anything interesting, you can do transcript level. But honestly speaking, I never needed to go to transcript level analysis. Ivo.