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,