Hi all,
This is the first time I'm trying to run a MIP (molecular inversion probe) library of ~800 genomic targets, dual index library in Novaseq.
The primers we use are custom primers for all reads (R1, R2, Ind). The Miseq run of the same pool looked like this (Miseq1, Miseq2 figures), while there was a fall in the first 50 bases of both R1 and R2 in the Novaseq run (Novaseq1, Novaseq2). Has anyone had any encounter with such phenomena and can suggest how to solve it? I heard an explanation of low hybridization efficiency of the custom primers in the Novaseq, but how can this explain the rest of the sequencing process?
Also, I'll be glad to hear from satisfied/non-satisfied Novaseq users general experience compared to other machines (namely Hiseq).
Many thanks!
This is the first time I'm trying to run a MIP (molecular inversion probe) library of ~800 genomic targets, dual index library in Novaseq.
The primers we use are custom primers for all reads (R1, R2, Ind). The Miseq run of the same pool looked like this (Miseq1, Miseq2 figures), while there was a fall in the first 50 bases of both R1 and R2 in the Novaseq run (Novaseq1, Novaseq2). Has anyone had any encounter with such phenomena and can suggest how to solve it? I heard an explanation of low hybridization efficiency of the custom primers in the Novaseq, but how can this explain the rest of the sequencing process?
Also, I'll be glad to hear from satisfied/non-satisfied Novaseq users general experience compared to other machines (namely Hiseq).
Many thanks!
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