genome-guided transcriptome mapping, genome or gene set?

Question

[402374688]

I have the genome of one species and the gene set as well. When aligning reads back to genome(gene set), which is better to use, genome or annotated gene set from genome? And what are their advantages and drawbacks? Thank you.

Answer 1

[EVR]

You can make use of GMAP or PASA or BLAT for aligning your gene set back to Genome.

[402374688]

Sorry but what is it used for?