I have total RNAseq data and one of my main goals is to map lncRNAs (long noncoding RNAs). I am using STAR for alignment and featureCounts for mapping (counting). For the lncRNAs, I think I need to use the annotation file gencode.v28.long_noncoding_RNAs.gtf.gz. I will pass this annotation file on to the counter featureCounts.
I have already created a Genome Index for STAR but using the different annotation file, with --genomeFastaFiles /home/inah/RefGTF/GRCh38/sequence/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/inah/RefGTF/GRCh38/annotation/Homo_sapiens.GRCh38.85.gtf .
My question is: Do I need to rerun STAR to create a Genome Index using the lncRNA annotation file gencode.v28.long_noncoding_RNAs.gtf.gz and then rerun STAR for the alignment before I run featureCounts with the lncRNA annotation file? Or can I just run featureCounts with the lncRNA annotation file using the STAR alignments obtained with the other annotation file? In other words, do I need to use the same annotation file for the aligner STAR and the counter featureCounts?