Daniel:Notebook/GenomeMiner/2013-9-25: Difference between revisions
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==Retrospective== | ==Retrospective== | ||
Given what we know now (that deletions are seriously undercounted using shortened reference files) | Given what we know now (that deletions are seriously undercounted using shortened reference files) |
Revision as of 22:20, 25 September 2013
Mock HL155 (Started 9/9/2013)
Mimic Data Using Short Reference (BWA)
Error Counting Results
Error Rate: 1.177% Error Rate of Insertions: 0.195% Error Rate of Deletions: 1.42e-06% Error Rate of Substitutions: 0.982%
Overview of Recent Results
Comparing Real Data
File:ProbeComparison Improved.png|File:AgilentMYCA ErrorComp090313.png |
Left: Uses full length reference file; Right: uses shortened reference files
Comparing Bowtie and BWA Reference File Length Data
Name | Pct Aligned | Subtitution Rate | Insertion Rate | Deletion Rate | Substitution Accuracy | Insertion Accuracy | Deletion Accuracy |
Mimic Data (Full Ref) BWA | 97.84 | 1.017 | 0.192 | 0.034 | 99.3 | 73.8 | 68.0 |
Mimic Data (Short Ref) BWA | 95.44 | 0.982 | 0.195 | 1.43E-06 | 97.2 | 75.0 | 0.0 |
Mimic Data (Full Ref) Bowtie | 95.47 | 0.887 | 0.195 | 5.52E-04 | 87.8 | 75.0 | 1.1 |
Mimic Data (Short Ref) Bowtie | 96.4 | 0.91 | 0.188 | 0.028 | 90.1 | 72.3 | 56.0 |
Actual | NA | 1.01 | 0.26 | 0.05 | NA | NA | NA |
File:Bowtie-BWA-Compare-092513.png
Retrospective
Given what we know now (that deletions are seriously undercounted using shortened reference files)