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

Question

[nash52]

Hi, I am trying to process RNA-seq data from fastq files to get raw counts using Galaxy. I want to use STAR for alignment purposes. However, I am not quite sure how to choose the associated gene model (gtf) file for splice junctions for the chosen reference genome. In Galaxy, there are two built-in options for humans: hg19 (full) and Human DEC. 2013 GRCh38/hg38 for reference genome. I want to use the hg19 (full) option. 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 selected hg19 reference genome? Thanks! Nash

[ermela.paparisto]

I am trying to do the same thing. Did you find an answer to your question by any chance? - Thank you, Ermela