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

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==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|Target list]]
***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; [[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]]
***Set I: gap size = 400-450bp, flanking len = 300bp
***Set II: gap size = 125-175bp, flanking len = 175bp

Latest revision as of 03:33, 19 March 2014