Hi. We have seen that for Nextera libraries, the smaller insert fragments cluster more efficiently than those with larger inserts. We ran our first 2x300 and most of the data is duplicated sequence as the inserts were ~300bp, despite seeing larger fragments (1kb) on the bioanalyzer.
To make better use of the 600-cycle v3, we want to try a size selection for Nextera. Has anyone attempted this? What did you try, and how successful were you? We were thinking of running the fragments on a gel either post-Zymo cleanup and isolating >600bp followed by PCR, or run the final library on a gel and isolating anything>600bp. Please share your experiences!
To make better use of the 600-cycle v3, we want to try a size selection for Nextera. Has anyone attempted this? What did you try, and how successful were you? We were thinking of running the fragments on a gel either post-Zymo cleanup and isolating >600bp followed by PCR, or run the final library on a gel and isolating anything>600bp. Please share your experiences!
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