I was wondering if it is possible to see RNAs in paired ended WGS data and didn't manage to find an answer to this question. Does anybody know whether you can see the signal from RNAs in whole genome sequencing data?
Considering how unstable RNA is, I think it would be difficult to get RNA contamination.
If you just want to spot-check, you can look at the coverage tracks for highly-expressed housekeeping genes. If there is RNA contamination, you should see higher coverage at the exons. WGS coverage should be fairly shallow, so RNA signal would be obvious.
Not sure if there is an easy systematic way to check. Probably the easiest is to compare the average coverage at coding regions to the whole genome.