Kun:LabNotes/MONOD/2015-7-16

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MONOD V6 (aka MONOD June2015)

Probe Design

  • Target selection:
   1. MONOD v1/v3 efficient targets
   2. BluePrint efficient targets
   3. Illumina/USC 1000 CRC targets
   4. Hand curated colon cancer methylation markers
   5. Hypermethylated genes from Hyen & Esteller NRG 2012 (Table 1&3)
   6. Commonly methylated genes from Ciriello et al NG 2013 (Figure 1C)
   7. Guo TCGA top 75 sites
   8. Guo TCGA NSCLC 5 sites
   9. Dana's gene list (BRCA1, MLH and related genes)
  • Design log: (Genome-miner: /home/kunzhang/CpgMIP/MONOD/June2015_probe_design)
   sort -k 1,1 -k 2,2n MONOD_June2015_all_targets_bed.txt | awk '{print $1"\t"$2"\t"$3}' | /home/kunzhang/softwares/bedtools-2.20/bin/bedtools merge -d 40 -i - > MONOD_June2015_all_targets_merged_bed.txt
   awk '{print $1":"$2"w\t"$1"\t"$2"\t"$3"\t+"'} MONOD_June2015_all_targets_merged_bed.txt > MONOD_June2015_all_targets_merged_ppDesigner.in
   awk '{print $1":"$2"c\t"$1"\t"$2"\t"$3"\t-"'} MONOD_June2015_all_targets_merged_bed.txt >> MONOD_June2015_all_targets_merged_ppDesigner.in
   split -l 1000 MONOD_June2015_all_targets_merged_ppDesigner.in MONOD_June2015_all_targets_merged_ppDesigner.in.
   sed 's/aa/ab/' < jobFile_June2015.pl > jobFile_June2015_ab.pl
   sed 's/aa/ac/' < jobFile_June2015.pl > jobFile_June2015_ac.pl
   sed 's/aa/ad/' < jobFile_June2015.pl > jobFile_June2015_ad.pl
   sed 's/aa/ae/' < jobFile_June2015.pl > jobFile_June2015_ae.pl
   sed 's/aa/af/' < jobFile_June2015.pl > jobFile_June2015_af.pl
   sed 's/aa/ag/' < jobFile_June2015.pl > jobFile_June2015_ag.pl
   sed 's/aa/ah/' < jobFile_June2015.pl > jobFile_June2015_ah.pl
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015.pl > June2015_probes.aa.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ab.pl > June2015_probes.ab.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ac.pl > June2015_probes.ac.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ad.pl > June2015_probes.ad.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ae.pl > June2015_probes.ae.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_af.pl > June2015_probes.af.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ag.pl > June2015_probes.ag.txt &
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl jobFile_June2015_ah.pl > June2015_probes.ah.txt &
   cat June*.txt > MONOD_June2015_all_targets_probeInfo.txt
   grep probes MONOD_June2015_all_targets_probeInfo.txt | awk '{print $1}' > MONOD_June2015_1st_design_failed_targets.txt
   match_column.pl MONOD_June2015_1st_design_failed_targets.txt MONOD_June2015_all_targets_merged_ppDesigner.in 1 > MONOD_June2015_all_targets_merged_ppDesigner_2nd.in
   # allow for up to 2 CpG sites per arm
   /home/kunzhang/softwares/ppDesigner_Kun_version/src/ppDesigner.pl  jobFile_June2015_2nd.pl > June2015_probes_2nd.txt &