Hi, we sequence samples using DNA prep with enrichment by illumina. They recommend an average fragment length of 350bp with a uniform electropherogram, usually reaching baseline around 500bp. We follow the protocol closely but have recently been ending up with final library mean fragment length of around 410 bp with an ugly looking electropherogram (attached) with the graph returning to baseline around 700bp. We know this is not a tagmentation issue and our hyb steps have not been changed. We are seeing a large coverage decrease, as well as a high fold 80 base penalty (>2). We suspect it might have something to do with the IPB cleanup, but cannot confirm until we receive a new lot. Can anyone help with this?
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