Kun:LabNotes/CpgSeq/2013-11-24: Difference between revisions
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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. | ||
**PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt]] | **PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt|Target list]] | ||
***Set I: gap size = 400-450bp, flanking len = 250bp | ***Set I: gap size = 400-450bp, flanking len = 250bp; [[Media:PANC_GBM_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script]] = [[Media:PANC_GBM_DMS_400bp_probes.txt|Probe sequences]]. | ||
***Set II: gap size = 125-175bp, flanking len = 125bp | ***Set II: gap size = 125-175bp, flanking len = 125bp; [[Media:PANC_GBM_DMS_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script]] = [[Media:PANC_GBM_DMS_1505bp_probes.txt|Probe sequences]]. | ||
**CRC_DMS: [[Media:targetFile_CRC_DMS.txt]] | **CRC_DMS: [[Media:targetFile_CRC_DMS.txt]] | ||
***Set I: gap size = 400-450bp, flanking len = 300bp | ***Set I: gap size = 400-450bp, flanking len = 300bp | ||
***Set II: gap size = 125-175bp, flanking len = 175bp | ***Set II: gap size = 125-175bp, flanking len = 175bp |
Revision as of 19:33, 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: Target list
- Set I: gap size = 400-450bp, flanking len = 250bp; ppDesigner Output + probe assembly script = Probe sequences.
- Set II: gap size = 125-175bp, flanking len = 125bp; ppDesigner Output + probe assembly script = Probe sequences.
- 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: Target list