When aligning reads with STAR, one can choose to project the alignment to the transcriptome as well.
In the end STAR writes one genome BAM file and one transcriptome BAM.
Afterwards, I pass the transcriptome BAM to rsem-calculate-expression for quantification.
Is it incorrect to the pass the genome BAM to RSeQC in this case instead of the transcriptome BAM? Or both would yield the same results?
(RSeQC requires a gene annotation file in BED format)
RELATED (but unanswered). RSEM BAM outputs, which one to use for RSeQC?