So I found that the annotated GTF file for hg19 from UCSC table does not adhere to the standard GTF format. Thus, I've been getting a fatal error in STAR:
Fatal INPUT FILE error, no valid exon lines in the GTF file: /work/cellbiology/s167125/Documents/ucsc_hg19/ucsc.hg19.gtf Solution: check the formatting of the GTF file. Most likely cause is the difference in chromosome naming between GTF and FASTA file.
I know that I can retrieve a good GTF file via genePredToGtf application but this is only compatible with Linux 64. I only have access to a Mac. I am wondering if there is an alternative method to retrieve a GTF for UCSC's hg19 reference genome.
Thank you for the help