With the announcement of the new micro and nano kits, is it better to use one of these with more cycles vs running the 2x26-bp for library validation? Granted the cost will be lower, and slightly faster, but will the extra cycles add any additional value?
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Just my opinion, but for library QC on the MiSeq before running it on a HiSeq, either of the new kits as 2x151 would give you much more useful information than a simple 2x26 run. The 2x26 run will let you know that you have libraries that will cluster and can be sequenced for both reads, but that's all that you know.
For a micro or nano 2x151, you get the same info as the 2x26 (library clusters, both reads can be sequenced) but you also get reads that will be very similar to what you'll see on the HiSeq. With the extra read length you can do things like examine insert size or calculate possible coverage for each sample in case you want to re-pool. The resulting reads can also be integrated into the final dataset while you wouldn't want to include data from a 2x26 run with a full 2x151 HiSeq run.
Given the cost difference, library QC with a full length micro or nano kit seems like it will ultimately give better data to judge the libraries with than a 2x26 run.
But this is all my opinion.
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