STAR needs genome file (*.fasta, fa) to create genome indexes. But, is it necessary to supplement the gtf annotation files, even though it works without it.
Details: I have a diploid genome and transcriptome database (made using reference genome, SNP/InDel polymorphism) of two different populations. The diploid genome is a single file but the population level transcriptome database aren't merged.
I think it can be merged but don't know of any consequences it may bring on the alignment. - Any suggestions??
If not the choice is just to create genome index and align the RNAseq data to it.
What difference does it make if you make the genome index with or without the gtf file?