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?
Guess that is a tough question. I would say that the tools wouldnt really go head to head on which one is better. But the real questions is 'what type of QC' is someone looking for. And this depends on the research question being asked from the RNA-seq data.
The common tools would do some things similarly, and it seems the results of that are pretty consistent. However, there are exclusive QC metrics or plots that make one tool more attractive than the other. Something on the lines of YMMV!
Hope that helps!