Abnormal coverage profile

Question

[Gary]

Hi, I use Qualimap2 (Okonechnikov et al. 2015) for our RNA-Seq quality analysis. Its coverage profile shows mean coverage profile of the transcripts. For example, our sample 1 could be normal, and sample 2 is RNA degradation, because a lot of reads mapped on the 3’. However, our sample 3 is abnormal, but not similar with the typical RNA degradation. Anybody can help me to understand what's wrong in our sample 3? Many thanks. Okonechnikov K, Conesa A, Garcia-Alcalde F. 2015. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics.