Using STAR aligner to build index of hg38

Question

[Grace]

Hi, I'm using STAR aligner to build index, and I want to use hg38 as reference genome.

But I think hg38 is DNA level. Can it also be used as a reference genome for RNAseq? (My data is RNAseq)

[Amitm]

Have you gone through the manual here. In addition to the genome fasta file, you would also need a GTF file (of gene annotations) to build the STAR index.

[Grace]

Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!

[GenoMax]

GTF file includes gene models/annotation information.

You could also use a program like salmon/kallisto with just human transcriptome to do similar analysis.

[Grace]

But I am going to do variant calling later, so I think STAR is more appropriate. Thank you.