Daniel:Notebook/GenomeMiner/2013-9-25: Difference between revisions

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[[Image:Bowtie-BWA-Compare-092513.png|800px]]


==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)

Back to Calendar

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)