We regularly perform 96 barcode Nextera XT and the results are usually pretty good. However the last run on the MiSeq gave us a cluster density of a bit less than 200k, and less than half of the fragments were >200 bp. We think this may have been due to insufficient mixing of fragments with beads during the initial AMpure cleanup.
Rather than wasting about £2500 in consumables, we were wondering if it might be possible to salvage this library. One idea was to re-pool from the storage plate and do a clean-up of the new pooled amplicon library, probably with AMpure as that's what we have available (e-Gel would be another idea but we don't have that in the lab). Any ideas on whether this is a good idea?
Then we might do a KAPA qPCR on the final library to ensure we get the dilution right for the DAL to get the clusters up.
Possible? Pointless? Your opinions appreciated!
Rather than wasting about £2500 in consumables, we were wondering if it might be possible to salvage this library. One idea was to re-pool from the storage plate and do a clean-up of the new pooled amplicon library, probably with AMpure as that's what we have available (e-Gel would be another idea but we don't have that in the lab). Any ideas on whether this is a good idea?
Then we might do a KAPA qPCR on the final library to ensure we get the dilution right for the DAL to get the clusters up.
Possible? Pointless? Your opinions appreciated!
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