Kun:LabNotes/CpgSeq/2013-11-24: Difference between revisions

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(Created page with "==Probe design for the NICE project== *Dinh went through one round of design using ppDesigner v1.1. However, upon close inspection, I found that some capturing arms contain lo...")
 
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*I modified get_probes.pl, and filtered out any candidate capturing arm that has over 6 A/T/G/Cs.  
*I modified get_probes.pl, and filtered out any candidate capturing arm that has over 6 A/T/G/Cs.  
*I repeated the probe design.  
*I repeated the probe design.  
**Set I: gap size = 400-450bp, flanking len = 250bp
**PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt]]
**Set II: gap size = 125-175bp, flanking len = 125bp
***Set I: gap size = 400-450bp, flanking len = 250bp
***Set II: gap size = 125-175bp, flanking len = 125bp
**CRC_DMS: [[Media:targetFile_CRC_DMS.txt]]
***Set I: gap size = 400-450bp, flanking len = 300bp
***Set II: gap size = 125-175bp, flanking len = 175bp

Revision as of 19:25, 24 November 2013

Probe design for the NICE project

  • Dinh went through one round of design using ppDesigner v1.1. However, upon close inspection, I found that some capturing arms contain long stretches of poly-Ts or poly-Gs.
  • I modified get_probes.pl, and filtered out any candidate capturing arm that has over 6 A/T/G/Cs.
  • I repeated the probe design.