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)
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.
Yes, I know also need a GTF file. So the GTF file will include RNA information?
Thanks for your answer!!
GTF file includes gene models/annotation information.
You could also use a program like salmon/kallisto with just human transcriptome to do similar analysis.
But I am going to do variant calling later, so I think STAR is more appropriate. Thank you.
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