GTF file in Ensembl database for RNA-Seq analysis

Question

[wangdp123]

Hi there,

I am using Ensembl gtf files to carry out RNA-Seq analysis.

I am interested in the expression levels of mRNA and long-noncoding RNAs in the data and I find that the gtf files contain not only mRNA and lncRNA but also a variety of non-coding RNAs such as miRNA, snoRNA, rRNA and misc_RNA.

My concern is whether I need to remove all the genes except for mRNA and lncRNA before performing the RNA-Seq analysis (e.g., mapping, expression quantification) for the purpose of my research?

Or I could keep all the types of genes in the gtf file and after the expression quantification I will be free to choose the types of genes of interest?

Which approach do you recommend and why?

Many thanks for your help,

Best regards,

Tom

Answer 1

[Benn]

Just keep everything on board. With a bit of luck you'll find that for example a novel snoRNA or miRNA is important in your research.