With questions about RNA-seq quality control often people suggest to use RNA-SeQC or CollectRnaSeqMetrics (from Picard), but no reason why to use that one instead of any of the other RNA-seq quality control measures. Some examples are Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?, http://seqanswers.com/forums/showthread.php?t=17073 and Which software do you use for RNA-seq data quality control?.
The last one is very similar to my question, but people give the methods they use without explaining why. I have not found any published comparisons between the methods. So why or when should I choose one method over the other?