I have some samples with total RNA Seq data and need to find differential expression. This is the first time I am working on this type of data and have no idea how to analyze it. I usually map the RNASeq data using tophat with say for mm9 around 21k refseq genes or so, then use HTSeq and DESeq to find differential expression. Now total RNA has more than the mRNA genes in it, what should I map this data to?
-
-
Hi ashuchawla,
If you want to do differential gene expression analysis, you can use the same pipeline. Mapping to mm9 is still fine.
AFAIK, the RefSeq annotation contains also more than mRNA. Just check your annotation. Personally, I prefer the Ensembl annotation which contains a lot of different biotype classes.
You can use for instance the IGV browser, load the Ensembl annotation via DAS and compare your mRNA-Seq data with the total RNA-Seq data.
Michael
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment