I want to know whether I have DNA contamination in my RNA-seq data. I have a library with DNAse and one without DNAse and another pair with additional treatment [DNAse(+) vs. DNAse(-), DNAse(+)+X vs. DNAse(-)+X]
1) Checking overall alignment rate of DNAse(+) vs. DNAse(-) and DNAse(+)+X vs. DNAse(-)+X] It is slightly higher on DNAse free samples
2) Checking alignment vs. transcripts It's all over the place - DNAse(+)+X has lowest rate, then DNAse(-) (without treatment), then DNAse(+) (without treatment) and finally the least background was in DNAse(-)+X... But I figured that might be due to rRNA? If it had not been sufficiently cleaned in some libraries it would not map to transcripts.
3) Looking at the reads in IGV after alignment to see if there is background/baseline in non-exon areas.
I am out of ideas, anyone know what else I can do?