I am just reading between the lines and assume that a pool of library was sequenced on both machines and a particular library yielded more reads on HiSeq than MiSeq. Some possible explanations:
1- different pooling ratio
2- differences in library size distribution
3- residual adapter in some libraries resulting in increased index hopping
I would do a demultiplexing of HiSeq reads with all index combinations to see if there has been unusual index hopping among some libraries (libraries with high index hopping will have less reads) and also pay attention to the number of unknown reads
1- different pooling ratio
2- differences in library size distribution
3- residual adapter in some libraries resulting in increased index hopping
I would do a demultiplexing of HiSeq reads with all index combinations to see if there has been unusual index hopping among some libraries (libraries with high index hopping will have less reads) and also pay attention to the number of unknown reads
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