http://gtc.wi.mit.edu/index.php?action=history&feed=atom&title=Compare_Pipeline_1.4vs1.3
Compare Pipeline 1.4vs1.3 - Revision history
2026-04-06T17:36:02Z
Revision history for this page on the wiki
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http://gtc.wi.mit.edu/index.php?title=Compare_Pipeline_1.4vs1.3&diff=17837&oldid=prev
Sgupta at 14:07, 29 May 2009
2009-05-29T14:07:57Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 14:07, 29 May 2009</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==<del class="diffchange diffchange-inline">Raw Reads</del>==</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>==<ins class="diffchange diffchange-inline">Comparing Solexa Pipeline Version 1.4 vs 1.3</ins>==</div></td></tr>
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Sgupta
http://gtc.wi.mit.edu/index.php?title=Compare_Pipeline_1.4vs1.3&diff=17836&oldid=prev
Sgupta at 14:06, 29 May 2009
2009-05-29T14:06:26Z
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<p><b>New page</b></p><div>==Raw Reads==<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: 1.4 seems to sometimes do a better job detecting raw clusters at lower densities.<br />
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| [[image:Raw_reads.JPG|center|thumb|1000px]]<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: As expected, 1.4 is able distinguish close clusters better than 1.3, hence intensities/clusters are more "pure".<br />
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| [[image:Fitered_reads.JPG|center|thumb|1000px]]<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: Number of filtered reads for 1.3 at a cluster density of around 100k (10 million reads) and drops somewhere between 160 - 170k. 1.4 seems to start dropping around 180k but in general it gives more reads as well as better quality reads.<br />
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| [[image:Density_vs_fitered_reads.JPG|center|thumb|1000px]]<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: Base quality starts to decrease drastically around 190k for 1.4. The optimal cluster density potentially is between 180 - 190k.<br />
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| [[image:Dataquality.JPG|center|thumb|1000px]]<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: Error Rates (to be added).<br />
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{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid black; height:100px" align="center"<br />
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| Conclusion: Alignment Rate (to be added).<br />
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Sgupta