demultiplexing multiple runs with and without samples same sample sheet

[seqtechno1]

Hello all,

I'm going to demultiplex a run with a sample sheet in which there are entries and adapter sequences in the sheet with no corresponding physical samples in the pool. I'm doing this for two reasons:

a. so that I don't have to modify the samplesheet and have multiple samplesheets for a project involving multiple sequencing runs (mitigate confusion)

b. I'm honestly curious how many 'reads' we will see after demultiplexing and what they represent. will they all originate from base calling error(s), or what would you call these (counts) I get after demultiplexing if, say, I get some very low number of counts for the sample which was not present?

[GenoMax]

If samples are truly absent then you may not get any reads assigned to them as long as your libraries are excellent quality and run has worked well.

That said if you allow errors during demultiplexing you may start seeing some reads getting assigned to the phantom samples. If that number is negligible then you can ignore those samples but if they start becoming significant you may have to go back and examine how your sample pools are being made (I assume they are being individually made independently?) and if there are any problems there.