Question: Reference genome and associated gene model (gtf, gff3) file for splice junctions in RNA STAR in Galaxy
gravatar for nash52
6 months ago by
United Kingdom
nash520 wrote:

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

ADD COMMENTlink modified 6 months ago • written 6 months ago by nash520

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

ADD REPLYlink written 18 days ago by ermela.paparisto0
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