QualiMap

Genomic Origin of reads

QualiMap generates various graphs to assist in the quality control of alignment sequencing data. It derives this information from GTF annotation files of the reference genome.

Figure 1 : genomic origin of reads for each sample.

source : MultiQC example RNAseq

This graph shows the genomic origin of the data. For RNAseq data, we expect a high proportion of reads from exons due to the transcriptomic nature of the RNA sequenced. The intragenic parts come from introns, and the intergenic regions include all the rest.