Are Illumina HiSeq 20500 and Illumina NovaSeq 6000 comparable?
Hi,
I am wondering if sequencing data generated using Illumina HiSeq 20500 are comparable to data generated using NovaSeq 6000?
I have some control samples sequenced using one system while treated samples using the other system, can I still looked for genes differentialy expressed? or they are not comparable?
Thank you!
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The batch effect between sequencing machines is typically minimal. The more important question is whether this is the only confounding factor. Have the samples been processed identically towards RNA extraction and library prep as well as on the same day? There must be a reason the samples have been sequenced on two machines, why is that? By the way it is a HiSeq 2500 not 20500.
I have some samples sequenced using NovaSeq6000, but due to the nature of the samples I don't have a sample control for them. I looked into a repository for control samples and found some data that can be useful but the sequencing was done with HiSeq 2500 (library prep was the same). Would them be comparable?