Hi Biostars,

When quantifying RNAseq expression with RSEM using a gff3 annotation file, does RSEM take into consideration the 'locus_tag' or 'Parent' field from the gff3? For example, if the 3-5 processed rRNA/tRNA transcripts within an rDNA locus have the same 'Parent' or 'locus_tag', are these taken into consideration during quantification? And if not, is there a simple way to force this using RSEM parameters (without pre-processing data)?

Thanks!