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Old 07-27-2017, 01:05 PM   #1
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Location: Oregon, USA

Join Date: Dec 2008
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Default Differences between HiSeq X and 3000/4000?

This document from 10X Genomics has made me pretty curious about the differences between the HiSeq X machines and the HiSeq 3000/4000.

I've been told by our Illumina engineer that they are basically the same instrument, so I am puzzled as to why the X would perform better than the 4000 for 10X Genomics libraries. I've looked at the cluster generation recipe files on our cBot for the X and the 4000, and determined that they are identical. Are the flowcells the same physical size? I've noticed that the official specs from Illumina list a lower cluster density for the X (12551412 K clusters/mm2) compared to the 4000 (13101524 K/mm2 passing filter), but the X gives a higher read number per flowcell. Is the X imaging a larger area in each lane?Are the recommendations for flowcell loading DNA concentrations the same? Could it be that the wells on the X flowcells are further apart than on the 4000 flowcells causing more bleeding of library fragments from well to well on the 4000 flowcells?

Has anyone sequenced the same library on the X and the 4000 and noted any differences? The specs for %>Q30 for PE150 are the same on both platforms. Is the real world performance any different?
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hiseq 4000, hiseq x

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