Differential expression analysis of lncRNA

Question

[analyst]

I have RNAseq data and I need to identify differential expression of lncRNA from RNAseq data. I am following this approach:

1. Alignment of RNA-seq data against reference genome using hisat2
2. Quantification of aligned reads through FeatureCounts (it outputs count file)

Now the question is how can I find the expression of lncrna from count file not mRNA.

Thanks a lot

[dthorbur]

Why have you just abandoned your previous post where you had generated discussion about this same topic?

Answer 1

[ATpoint]

It's exactly the same as any RNA-seq analysis. The GTF file for your organism tells you which genes are lncRNAs. I would just quantify reads against transcriptome with salmon, then go with tximport to get gene level counts and then any downstream DE tool. It's not all all different to what we always do in RNA-seq, just that interpretation is harder since for lncRNAs there are barely no functional annotations available.

[analyst]

Thanks a lot ATpoint! Do you mean that I should grep only lncRNA from reference gtf file and use that?

grep "lncRNA" AT10.58.gtf > lncRNA.gtf