Daniel:Notebook/GenomeMiner/2013-9-25: Difference between revisions
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>Djacobse (Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ===Error Counting Results=== Error Rate: 1.177% ...") |
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
==Mimic Data Using Short Reference (BWA)== | |||
===Error Counting Results=== | ===Error Counting Results=== | ||
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Error Rate of Deletions: 1.42e-06% | Error Rate of Deletions: 1.42e-06% | ||
Error Rate of Substitutions: 0.982% | Error Rate of Substitutions: 0.982% | ||
==Overview of Recent Results== | |||
===Comparing Real Data=== | |||
{|Class="wikitable" | |||
|[[Image:ProbeComparison Improved.png|500px]]|[[Image:AgilentMYCA ErrorComp090313.png|500px]] | |||
|} | |||
'''Left''': Uses full length reference file; '''Right''': uses shortened reference files | |||
===Comparing Bowtie and BWA Reference File Length Data=== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt;font-weight:bold" align="center" valign="bottom" | |||
| width="174" height="30" | Name | |||
| width="65" | Pct Aligned | |||
| width="65" | Subtitution Rate | |||
| width="65" | Insertion Rate | |||
| width="65" | Deletion Rate | |||
| width="85" | Substitution Accuracy | |||
| width="65" | Insertion Accuracy | |||
| width="65" | Deletion Accuracy | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Mimic Data (Full Ref) BWA | |||
| align="center" align="center" valign="bottom" | 97.84 | |||
| align="center" align="center" valign="bottom" | 1.017 | |||
| align="center" align="center" valign="bottom" | 0.192 | |||
| align="center" align="center" valign="bottom" | 0.034 | |||
| align="center" align="center" valign="bottom" | 99.3 | |||
| align="center" align="center" valign="bottom" | 73.8 | |||
| align="center" align="center" valign="bottom" | 68.0 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Mimic Data (Short Ref) BWA | |||
| align="center" align="center" | 95.44 | |||
| align="center" align="center" | 0.982 | |||
| align="center" align="center" | 0.195 | |||
| align="center" align="center" | 1.43E-06 | |||
| align="center" align="center" valign="bottom" | 97.2 | |||
| align="center" align="center" valign="bottom" | 75.0 | |||
| align="center" align="center" valign="bottom" | 0.0 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Mimic Data (Full Ref) Bowtie | |||
| align="center" align="center" | 95.47 | |||
| align="center" align="center" | 0.887 | |||
| align="center" align="center" | 0.195 | |||
| align="center" align="center" | 5.52E-04 | |||
| align="center" align="center" valign="bottom" | 87.8 | |||
| align="center" align="center" valign="bottom" | 75.0 | |||
| align="center" align="center" valign="bottom" | 1.1 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Mimic Data (Short Ref) Bowtie | |||
| align="center" align="center" | 96.4 | |||
| align="center" align="center" | 0.91 | |||
| align="center" align="center" | 0.188 | |||
| align="center" align="center" | 0.028 | |||
| align="center" align="center" valign="bottom" | 90.1 | |||
| align="center" align="center" valign="bottom" | 72.3 | |||
| align="center" align="center" valign="bottom" | 56.0 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Actual | |||
| align="center" valign="bottom" | NA | |||
| align="center" align="center" valign="bottom" | 1.01 | |||
| align="center" align="center" valign="bottom" | 0.26 | |||
| align="center" align="center" valign="bottom" | 0.05 | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
|} | |||
[[Image:Bowtie-BWA-Compare-092513.png|800px]] | |||
===Discussion=== | |||
From above, we can see that both Bowtie and BWA do not count deletions accurately without the given reference sequence. So, looking back at the original data, it now makes sense that using the shortened reference sequence had fewer errors. At the time, we thought it was good that the error decreased. However, the majority of the errors lost were deletions, and the mock sequence data has shown that deletions are seriously undercounted using the shortened reference sequences. It's likely, therefore, that the original error counting was more accurate. |
Latest revision as of 22:25, 25 September 2013
Mock HL155 (Started 9/9/2013)[edit]
Mimic Data Using Short Reference (BWA)[edit]
Error Counting Results[edit]
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[edit]
Comparing Real Data[edit]
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[edit]
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
Discussion[edit]
From above, we can see that both Bowtie and BWA do not count deletions accurately without the given reference sequence. So, looking back at the original data, it now makes sense that using the shortened reference sequence had fewer errors. At the time, we thought it was good that the error decreased. However, the majority of the errors lost were deletions, and the mock sequence data has shown that deletions are seriously undercounted using the shortened reference sequences. It's likely, therefore, that the original error counting was more accurate.