Reference genome and associated gene model (gtf, gff3) file for splice junctions in RNA STAR

Can I use the gencode v19 annotation gtf file or any genecode version annotation gtf file for GRCh37 assembly as the associated gene model file for splice junctions for the built-in hg19 reference genome?

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Hello @nash52

Yes, Gencode’s human annotation for build GRCh37 is a match for UCSC’s hg19 version of the assembly.

For the how-to, please see:

Q&A (same formatting advice applies to hg19): RNA-STAR and hg38 GTF reference annotation



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