Partial or compelte string matches in STAR parameters

[Peter Tam]

Hi Alex,

I am using GFF3 annotation to generate a genome index for subsequent RNA-seq mapping. I see that the sjdbGTFtagExonParentGene parameter is set with "gene_id" as default.

My question is whether STAR performs an exact match or partial match to look for "gene_id" in each exon line? For example, if I have got two attributes like "gene_id" and "gene_id_platform", will STAR be able to detect the contents of "gene_id" and not "gene_id_platform" for genome indexing?

Thanks in advance,

Peter

[Alexander Dobin]

Hi Peter,

STAR only looks for a complete match.