You can use FastQC to perform basic QC of your BAM file (See Pre-Alignment QC). This will give you output very similar to when you ran FastQC on your fastq files. Background: RSeQC is a tool that can ...

#2-iv. Post-Alignment QC ##Use samtools, samstat, and FastQC to evaluate the alignments ##Using FastQC You can use FastQC to perform basic QC of your accepted_hits.bam file (See Pre-Alignment QC).