RSeQC is used a lot, but I find QoRTs 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 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
FASTQC is primarily for pre-alignment and it takes as input FASTQ or FASTA files. After you perform your alignment, you should have produced a SAM or BAM file, which are not used as input for FASTQC.
The most common quality control metric that is used post-alignment is to check how many of your reads have aligned to the reference genome. The command
samtools mpileup produces this.