Daniel:Notebook/GenomeMiner/2013-9-3

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Revision as of 22:52, 5 September 2013 by >Djacobse (→‎HL155)
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HL155

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Matt discovered that the MYcroarray probe set may not be aligning well due because we should be aligning to the reverse complement of the probe sequences we've been using. As such, Matt did the analysis, and the results changed fairly dramatically.

Error Comparison

  V4S1 V4S2 V4S3 V4S4 V6S1 V6S2 V6S3 V6S4 Weighted Average (%)
Overall Error Rate 1.33% 1.32% 1.32% 1.19% 1.17% 1.13% 1.18% 1.15% 1.19
Insertions 0.26% 0.21% 0.24% 0.24% 0.19% 0.18% 0.19% 0.21% 0.20
Deletions 0.05% 0.04% 0.04% 0.05% 0.04% 0.04% 0.04% 0.05% 0.04
Substitutions 1.01% 1.07% 1.04% 0.90% 0.94% 0.91% 0.95% 0.89% 0.94
Number of Probes 2959 3600 5850 5987 16559 16400 13000 13314  

Updated Error Comparison

File:AgilentMYCA ErrorComp090313.png

So now MYcroarray is still the worst of the three companies, but does not have nearly as bad of error.

Probecounts

It's also important to count the probes again with the updated reverse complementary info.

Workflow