I am looking at the presence of viral genotypes within individual samples within an assay. Often times there is a sample whose read counts are firing off the charts and this sample tends to "bleed through" to the other samples.
I have recently tried confronting this problem with chi square analysis of conditional probability. For instance let's say I observe with 10 sample viral genotypes A and B. I then calculate the expected number of samples having both genotypes A and B from the number of A positive samples and number of B positive samples.
So far this is all I have. I do not know if anyone else has any ideas on how to determine and quantify bleed through in viral genotyping.
Slightly more information about this situation: these samples were run on Illumina HiSeq, we are planning on doing another HiSeq run with even more samples shortly so would like to take proper precautions with that, additionally the current pipeline utilizes Novobarcode as a demultiplexer so if anyone has suggestions on what I can implement during processing to minimize the effect of cross contamination that'd be helpful.