Daniel:Notebook/GenomeMiner/2013-9-25: Difference between revisions
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===Comparing Bowtie and BWA Reference File Length Data=== | ===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+00 | |||
| 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 | |||
|} | |||
==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 22:12, 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+00 | 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 |
Retrospective
Given what we know now (that deletions are seriously undercounted using shortened reference files)