Hey, sorry to dredge this thread up again, but I have another question! Illumina recommend a double-Ampure cleanup after ligation with a 1:1 ratio of Ampure. This confused me way back when I started this thread, but now I realize that as well as cleaning up the reaction this is also a way of removing DNA below about 140bp - adapters and adapter dimers, in other words.
So here's my next question: Can I save time by doing a different cleanup at this step (e.g. QIAQuick PCR Purification) if I'm going to do downstream exome capture? I'm assuming that the exome capture step will be largely unaffected by the adapter dimers. Or have I overlooked something?
So here's my next question: Can I save time by doing a different cleanup at this step (e.g. QIAQuick PCR Purification) if I'm going to do downstream exome capture? I'm assuming that the exome capture step will be largely unaffected by the adapter dimers. Or have I overlooked something?
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