I am using human transcriptome as a reference for RNA-Seq data. I am done with the alignment of all the samples. For the post-alignment QC, I am aware RSeQC is widely used. However, almost all the parameters require the gene annotation file for that. Since I used transcriptome as a reference I did not use gene annotation gtf file. I am wondering what are the after alignment QC parameters I should test? and using which tool in this particular case.
Thank you in advance.