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?
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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
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