Problem of unmapped reads

[hypno]

Dear all,
I have problem to align my RNA-seq experiments. FAstq show not low quality but however I have very low allign 50%. How can understand if the problem are related with some contaminants (?) or to my gtf file?
RNA seq 2x100 PE from FPE samples I allign using topath hg19 ( 60ML reads).

Exist a way to check the quality of my library after allignmen (complexity?)
thanks for your help!

[TiborNagy]

You can use samtools idxstats, but it is hard to tell what would be wrong (contamination or wrong annotation).