lncRNA quantification featurecounts

Question

[Beth]

Hi everyone, I want to analyze the differential expression of lncRNA using TCGA data processed with RSubread (FPKM and TPM, gene-level data, see here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804769/).

Is there any way to filter only lncRNA gene IDs from the output of featurecounts? And would it be relevant to use the values (counted with gene id) in the DE analysis of lncRNA?

Thank you in advance.

[Hamid Ghaedi]

You can use gene-level raw read counts for DE. For the lncRNA list, you may subset the expression dataset rownames (suppose to hold ENSG ids) by the gene biotype. To do so use biomaRt to find biotype for each gene, then only retain lncRNA.

Answer 1

[swbarnes2]

I think you need at analyze everything together, then after you get your fold changes and p values, then you can look at the subset you care about.

Answer 2

[Zhenyu Zhang]

Some lincRNA is in the Ensembl gene model, and they are structurally similar to mRNA. So they might have already been quantified in the mRNA quantification data