Hello,

I am trying to find a qc package to be used with.bam files.  In using the  RNA-SeQC package I ran into difficulty because it required -s, -r, and -r arguments.  I only have a .bam file and do not have these required parameters.  

Is there a RNA-Seq specific QC tool where I can simply point to the .bam file and have it create a qc report?  

Thank you.


[RSeQC](http://rseqc.sourceforge.net/), [QoRTs](https://hartleys.github.io/QoRTs/), [BamQC](https://github.com/s-andrews/BamQC) are all valid options.

However, I'm surprised you cannot use RNA-seQC, because in its description it says: "RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files."