Hello,

I have aligned the RNA-seq data to the human genome and I used FASTQC for the pre-processing data. Can I use FASTQC for post alignment QC also? Or is there a better way of doing it?


Thank you in advance.
RSeQC is used a lot, but I find [QoRTs](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506620/) a bit more user-friendly, especially if you have numerous samples. 

In addition, feeding the results of a) FastQC, b) STAR (or whatever aligner you've used), and c) featureCounts to [MultiQC](http://multiqc.info/docs/) is already quite useful.

The typical things you want to look out for:

* at least 80% alignment rate
* not too many intronic/intergenic reads
* even gene body coverage
