Filtering lncRNAs from total RNA

Question

[mropri]

I am trying to analyze data from patient samples. I took the data of RNA seq from this paper: https://www.mdpi.com/2075-4426/9/2/18/htm

I want to look at specifically lncRNAs and how they change from normal to cancer cells. I have done alignment using STAR and ran DEseq2 for differential expression on total RNA. I was wondering if there is a way to filter out only lncRNAs and look at differential expression for those. Any help is appreciated.

[Santosh Anand]

1. download the Gencode annotation https://www.gencodegenes.org/

2. Get the respective biotypes of all the genes https://www.gencodegenes.org/pages/biotypes.html

3. and filter according to the biotypes you need. You may need to run the DESeq again on the filtered set only

[GenoMax]

lncRNA GTF file is available separately at GENCODE. No need to separate out biotypes.

[mropri]

How do I use the lncRNA gtf file to filter out the lncRNAs from the total RNA that I have aligned using STAR. Hope you can provide a little detail. I am new to RNA seq so any help is appreciated.