Filtering lncRNAs from total RNA
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.
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download the Gencode annotation https://www.gencodegenes.org/
Get the respective biotypes of all the genes https://www.gencodegenes.org/pages/biotypes.html
and filter according to the biotypes you need. You may need to run the DESeq again on the filtered set only
lncRNA GTF file is available separately at GENCODE. No need to separate out biotypes.
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.