I was doing a quality check of bam file output of STAR alignment in RNASeq analysis. I selected RSeQC for the same and here I paste the output of bam_stat.py command:
#========================================= # All numbers are READ count #========================================= Total records: 37463450 QC failed: 0 Optical/PCR duplicate: 0 Non primary hits 9558982 Unmapped reads: 0 mapq < mapq_cut (non-unique): 4344540 mapq >= mapq_cut (unique): 23559928 Read-1: 0 Read-2: 0 Reads map to '+': 11778663 Reads map to '-': 11781265 Non-splice reads: 19519751 Splice reads: 4040177 Reads mapped in proper pairs: 0 Proper-paired reads map to different chrom:0
How do I evaluate the quality of the alignment from the above report ? Kindly guide.