Kun:LabNotes/MONOD/2015-7-16: Difference between revisions
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./[[Media:get_small_insert_count_matrix_2015-7-16.txt|get_small_insert_count_matrix.pl]] > [[Media:150721_MiSeq_small_insert_count_matrix.txt|150721_MiSeq_small_insert_count_matrix.txt]] | ./[[Media:get_small_insert_count_matrix_2015-7-16.txt|get_small_insert_count_matrix.pl]] > [[Media:150721_MiSeq_small_insert_count_matrix.txt|150721_MiSeq_small_insert_count_matrix.txt]] | ||
*I then take the top 100 probes with the most target-independent circularization events, and did the clustering with R. | *I then take the top 100 probes with the most target-independent circularization events, and did the clustering with R. | ||
x=read.table("150721_MiSeq_small_insert_count_matrix_top100.txt",header=TRUE,row.names=1); | x=read.table("[[Media:150721_MiSeq_small_insert_count_matrix_top100.txt|150721_MiSeq_small_insert_count_matrix_top100.txt]]",header=TRUE,row.names=1); | ||
library(gplots) | library(gplots) | ||
heatmap.2(as.matrix(log10(x+1)),scale="none", key=T, symkey=F,density.info="none",trace="none",dendrogram="both",Rowv=TRUE,Colv=TRUE, cexCol=0.6, cexRow=0.3) | |||
[[Media:150721_MiSeq_small_insert_count_top100_heatmap.pdf|Hi-Res PDF]] | [[Media:150721_MiSeq_small_insert_count_top100_heatmap.pdf|Hi-Res PDF]] | ||
[[Image:150721_MiSeq_small_insert_count_top100_heatmap.png|500px]] | [[Image:150721_MiSeq_small_insert_count_top100_heatmap.png|500px]] |
Revision as of 22:37, 23 July 2015
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 &
- Assembled with the V6 amplification adaptors.
- ProbeInfo file: Media:MONOD_June2015_all_targets_probeInfo.txt
- Oligo sequences: Media:MONOD_Jun2015_sequence.txt
Experiments
First test
- Dinh did the first test:Dinh/Dinh_2015/NOTES/2015-6-25.
- The sequencing data are in genome-miner: /media/LTS_33T/SeqStore2/150721_MiSeq
- I did the checking for target-independent circularization, by taking 100,
#in the working directory: /home/kunzhang/CpgMIP/MONOD/Data/150721_MiSeq ./batch_map_N_parse.pl ./get_small_insert_count_matrix.pl > 150721_MiSeq_small_insert_count_matrix.txt
- I then take the top 100 probes with the most target-independent circularization events, and did the clustering with R.
x=read.table("150721_MiSeq_small_insert_count_matrix_top100.txt",header=TRUE,row.names=1); library(gplots) heatmap.2(as.matrix(log10(x+1)),scale="none", key=T, symkey=F,density.info="none",trace="none",dendrogram="both",Rowv=TRUE,Colv=TRUE, cexCol=0.6, cexRow=0.3)
Hi-Res PDF File:150721 MiSeq small insert count top100 heatmap.png