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Old 02-19-2019, 07:46 AM   #1
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Location: Massachusetts

Join Date: Jul 2018
Posts: 6
Question NextSeq - proportional sequencing of different fragment sizes on the same run


I'm still learning the boundaries of the NextSeq and was wondering if anyone had experience with the following or advice where I could find more information.

I am trying to optimize run space on our Illumina NextSeq and combine multiple projects including 275bp amplicons and 400bp metagenomic libraries (bp not including adaptor/barcode lengths) into one HT run. My issue is getting predictable coverage of each project; the competitive binding of smaller fragments usually means I end up with way more coverage of the small amplicons than I originally allocated space to and not enough coverage of the metagenomes.

Is there a more accurate method to calculate the division of the run?

Thank you
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