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.
- PANC_GBM_DMS: Media:targetFile_PANC_GBM_DMS.txt
- 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
- PANC_GBM_DMS: Media:targetFile_PANC_GBM_DMS.txt