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Old 04-30-2015, 03:37 AM   #59
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Location: London

Join Date: Jun 2009
Posts: 298

I asked the same question to Illumina Tech Support last week. Here's their response.

"Besides the changes in the software, there was a significant change in the v2 reagents. We changed the dyes of each base to improve the base call and overall sequencing data. This means that we have changed Q30 tables and other features in the software. Overall we do not recommend to compare data obtained between different versions of software.

Depending on which application, experimental design and data analysis workflow you may not have significatnt differences. It is your choice to set up the appropriate controls and technical/biological replicates.

The best test is to re-sequence a sample with v2 reagents that you have sequenced before with v1 reagents and compare directly the results. "
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