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Old 04-19-2016, 03:07 PM   #5
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Location: boulder, co

Join Date: Aug 2012
Posts: 5

This is super easy, we have done it multiple times with no issue besides needing to buy a longer read on Illumina. Just take your ion torrent library as is and put it through the truseq kit, having the ion adapters/barcodes on the ends isnt any different than having a DNA fragment of that size. Since the adapters are different and the barcodes are sequenced differently by illumina there is no conflict. I would not do what the post above my says unless you want to add a lot more pcr bias and unnecessary work to your life. to avoid issues with end diversity just spike in 10-15% phix into the library before sequencing, and if your still concerned we commonly use a "diversity spike" which is just a amplicon with end diversity (such as custom barcodes like 8 base barcode and the first 20 bases of the fusion primer) we spike into the sample with limited end diversity.
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