Daniel:Notebook/GenomeMiner/2013-9-3: Difference between revisions
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[[Matt:LabNotes/2013-8-30|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. | [[Matt:LabNotes/2013-8-30|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== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | ||
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So now MYcroarray is still the worst of the three companies, but does not have nearly as bad of error. | 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=== |
Revision as of 22:52, 5 September 2013
HL155
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.