I'm working with RNA-seq data (tumor tissues sampled from female and male patients). After mapping, only 29-55% of reads are assigned to exons, and 39-60% are unassined-MultiMapped. Is this reasonable for RNA-seq data?
I also checked the number of reads mapped to each chromosome. Some of the samples have very high mapping on chromosome M, 21, 7, 1 and 22. I thought this has to do with the nature of tumors (in this case colon) and the fact that mitochondrial DNA alterations have been widely reported in many tumors. Am I correct or there's something wrong with my data or analysis?
I do appreciate your kind help.