How will contaminating Rd reads map onto NP?

Based on the analysis in the previous post, we can do the lower-bound and upper-bound calculations and corrections for each of our 12 'uptake' samples (3 replicates each of 4 treatments). This will give us good estimates of the % Rd contamination for each sample. But what do we do with this information?We can map each sample just to its own NP genome (or GG). Now the Rd-derived reads from positions that have strong similarity to NP locations should map there, including all the repeats and no-SNP reads.  I think that the Rd-derived sequences that don't have NP homologs and thus can't be mapped onto NP will be given Q=0 scores. This will be about 10-15% of the Rd reads (a known value). So most NP positions will have their NP read coverage plus (say) 20% extra coverage from the Rd reads. But some NP positions (again 10-15%) don't have Rd homologs, and these will have only their NP coverage.Grad student and former postdoc, how should we handle this?
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs