Kun:LabNotes/CpgSeq/2013-11-24: Difference between revisions
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**PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt|Target list]] | **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:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:PANC_GBM_DMS_400bp_probes.txt|Probe sequences]]: 3,514 probes | ***Set I: gap size = 400-450bp, flanking len = 250bp; [[Media:PANC_GBM_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:PANC_GBM_DMS_400bp_probes.txt|Probe sequences]]: 3,514 probes | ||
***Set II: gap size = 125-175bp, flanking len = 125bp; [[Media:PANC_GBM_DMS_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:PANC_GBM_DMS_1505bp_probes.txt|Probe sequences]] | ***Set II: gap size = 125-175bp, flanking len = 125bp; [[Media:PANC_GBM_DMS_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:PANC_GBM_DMS_1505bp_probes.txt|Probe sequences]]: 6,960 probes | ||
**CRC_DMS: [[Media:targetFile_CRC_DMS.txt]] | **CRC_DMS: [[Media:targetFile_CRC_DMS.txt]]. | ||
***Set I: gap size = 400-450bp, flanking len = 300bp; [[Media:CRC_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:CRC_DMS_400bp_probes.txt|Probe sequences]]: 148 probes | ***Set I: gap size = 400-450bp, flanking len = 300bp; [[Media:CRC_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:CRC_DMS_400bp_probes.txt|Probe sequences]]: 148 probes | ||
***Set II: gap size = 125-175bp, flanking len = 175bp; [[Media:CRC_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:CRC_DMS_1505bp_probes.txt|Probe sequences]]: 149 probes | ***Set II: gap size = 125-175bp, flanking len = 175bp; [[Media:CRC_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:CRC_DMS_1505bp_probes.txt|Probe sequences]]: 149 probes |
Revision as of 20:39, 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 V6 = Probe sequences: 3,514 probes
- Set II: gap size = 125-175bp, flanking len = 125bp; ppDesigner Output + probe assembly script V4 = Probe sequences: 6,960 probes
- CRC_DMS: Media:targetFile_CRC_DMS.txt.
- Set I: gap size = 400-450bp, flanking len = 300bp; ppDesigner Output + probe assembly script V6 = Probe sequences: 148 probes
- Set II: gap size = 125-175bp, flanking len = 175bp; ppDesigner Output + probe assembly script V4 = Probe sequences: 149 probes
- PANC_GBM_DMS: Target list