Ns126:Calendar/NOTES/2015-8-31: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
No edit summary
>Shicheng
 
(55 intermediate revisions by the same user not shown)
Line 1: Line 1:




== Compare methylation haplotype region with Hic Data==


* liftover epigenetic annotation from hg18 to hg19
* liftover epigenetic annotation from hg18 to hg19
Line 13: Line 14:
** Annotation Database:[[File:R20150831.BedEnrichment.Annaotation.Database.hg19.txt]]
** Annotation Database:[[File:R20150831.BedEnrichment.Annaotation.Database.hg19.txt]]
* Tissue specific methylation haplotype region analysis
* Tissue specific methylation haplotype region analysis
*[[Samples List]]
* Dr. Zhang told me to remove H1,Cancer tissues. therefore only 49 sample were included (3 Heyn, 10 N37 and 36 salk) [[Samples List]]


*[[File:Code.20190903.TSI.22.tissues.R.txt]]
*[[File:Code.20190903.TSI.22.tissues.R.txt]]
<gallery width=400px height=400px>
<gallery widths=400px heights=400px>
File:GSI.22.tissues.png|Figure. Heatmap of normal tissues by high GSI regions.
File:GSI.22.tissues.png|Figure. Heatmap of normal tissues by high GSI regions.
</gallery>
</gallery>
*the methylation haplotype regions in above figure see [[File:High.gsi.genome.cor.txt]]
/home/sguo/monod/phase2/high.gsi.genome.cor.txt
*




== compare the cluster analysis with raw methylation signal==
== Compare the cluster analysis with raw methylation signal==


=== achieve raw methylFreq files ===
=== Achieve raw methylFreq files ===


I found the overlapped CpG sites between methylation haplotype and raw methylFreq (depth>5) was only 49. The reason when we calculate the methylation haplotype we did not get rid of low coverage reads. Therefore, I need collect the raw methylation methylFreq file and merage them again without low coverage reads discarding.  
*I found the overlapped CpG sites between methylation haplotype and raw methylFreq (depth>5) was only 49. The reason when we calculate the methylation haplotype we did not get rid of low coverage reads. Therefore, I need collect the raw methylation methylFreq file and merage them again without low coverage reads discarding.  
After discuss with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)
*After discussing with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)
* 651 CpG sites were found overlapped with 180 high GSI methylation haplotype regions. among them, 35 sites were found have more than 30% missing value and then were filtered in the further analysis.
* the heatmap based on raw methylation signals were as the following(right). [[File:Heatmap.RawSignal.High.GSI.R.txt]]
[[File:GSI.RRBS.BSPP.WGBS.RawSignal.png|800px]]
 
==Comare MHL and Average methylation level==
 
* Bam to methyhaplotype
* I found a problem, I do not know why non-CG would occur in methyhplot and why position would occur multiple time. You can try the following command:
grep chr6:53658269-53659397 /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/BSPP/mld_block_stringent_hapInfo/NC-23.WGBS_BSPP.mld_blocks_r2-0.5.hapInfo.txt
 
 
cd /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_stringent_hapInfo
 
head 6-P-10.mld_blocks_r2-0.5.hapInfo.txt
 
chr10:100027865-100027869    TTT    2    100027865,100027867,100027869
chr10:100027897-100027992    TTTTT    17    100027957,100027961,100027981,100027988,100027992
chr10:100027897-100027992    GTTTT    1    100027927,100027930,100027938,100027944,100027957
chr10:100027897-100027992    TTTTTTTTT    15 100027908,100027918,100027922,100027925,100027927,100027930,100027938,100027944,100027957
chr10:100027897-100027992    TTT    2    100027897,100027899,100027908
chr10:100174838-100174961    TTT    2    100174838,100174852,100174875
chr10:100227297-100227560    TTTTT    10    100227438,100227445,100227449,100227466,100227488
chr10:100227297-100227560    TCTCT    1    100227438,100227445,100227449,100227466,100227488
chr10:100227297-100227560    TTTT    4    100227445,100227449,100227466,100227488
chr10:100227297-100227560    TTTTC    1    100227438,100227445,100227449,100227466,100227488
 
cd /media/Ext12T/DD_Ext12T/RRBS_MONOD/Bam_Merged/
samtools view 6-P-10.merged.bam chr10:100027865-100027869
 
cd /media/Ext12T/DD_Ext12T/RRBS_MONOD/Bam_Merged/
samtools view 6-P-1.merged.bam chr10:101089382-101089519 | less -S
 
cd /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_stringent_hapInfo
head
 
=== Update new MHL===
 
====Code and Data====
Code: [[File:Get methHap load matrix 01Oct2015.txt]]
All WGBS data: /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_Oct2015.txt
All RRBS data:/home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_Oct2015.txt
All WGBS-SeqCap data: /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_Oct2015.txt
 
* methylation block regions (bed files for each chrosome and complete regions)
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr*.mld_blocks_r2-0.5.bed
 
* specific loop in the pbs script
cd /oasis/tscc/scratch/k4zhang/MONOD/hESC_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr2.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/BAMfiles/methylC-seq_h1_r2.chr2.rmdup.bam > methylC-seq_h1_r2.chr2.hapInfo.txt
 
cd /oasis/tscc/scratch/k4zhang/MONOD/Ecker_Tissue_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr10.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/BAMfiles/STL001BL-01.chr10.sorted.clipped.bam > STL001BL-01.chr10.hapInfo.txt
 
cd /oasis/tscc/scratch/k4zhang/MONOD/N37_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chrX.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/BAMfiles/Indx22.chrX.rmdup.bam > N37-Stomach.chrX.hapInfo.txt
 
cd /oasis/tscc/scratch/k4zhang/MONOD/tumor_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr8.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/HCT116.chr8.sorted.clipped.bam > HCT116.chr8.hapInfo.txt
 
* the summarized samples are as the following:
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr1.mld_blocks_r2-0.5.bed
/home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/N37_10_tissue_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/tumor_WGBS_sample_info_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/H1ESC_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/RRBS_merge/1407_RRBS_merbed_sampleInfo__WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/SeqCap/WGBS_SeqCap_plasma_sample_info.txt
/home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/TSCC_whole_blood_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/Ecker_Tissue_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/WGBS_BSPP/WGBS_BSPP_sample_info.txt    # remember to delete \n before use
 
cp /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr1.mld_blocks_r2-0.5.bed /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/N37_10_tissue_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/tumor_WGBS_sample_info_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/H1ESC_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/RRBS_merge/1407_RRBS_merbed_sampleInfo__WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/SeqCap/WGBS_SeqCap_plasma_sample_info.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/Ecker_Tissue_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/TSCC_whole_blood_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/WGBS_BSPP/WGBS_BSPP_sample_info.txt /home/shg047/monod/haplo
perl -p -i -e 's/MONOD\n/MONOD/g' WGBS_BSPP_sample_info.txt
 
 
=== methyhaplotype to matrix===
* transfer haplotype result (per chrosome per sample) to genome miner
 
* methylation haplotype load (mhl) matrix
cp /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/
cp /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/
cp /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_Oct2015.txt  /home/shg047/monod/oct/data/
* [[tissue specific mhl regions]]
 
* extract raw methylation signals within above regions(multiple cpg site in each regions)
** [[extract CpG site within above regions]]
 
* extract absolute methylation levels within above regions(one value in each regions)
 
* Bam files: ESC, Ecker, N37, age, Plasma were in the TSCC center
/home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/BAMfiles/
/home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/BAMfiles
/home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/BAMfiles
/home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/
/home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/
 
* # chr17:16955467-16955609 in Colon_primary_tumor.chr17.sorted.clipped.bam
samtools tview -p chr17:16955467 /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/Colon_primary_tumor.chr17.sorted.clipped.bam  /home/shg047/db/hg19.fa
* # chr11:110910907-110910951 in middle-age.chr11.rmdup.bam
samtools tview -p chr11:110910907 /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/middle-age.chr11.rmdup.bam /home/shg047/db/hg19.fa
* # grep chr11:110910907-110910951 in hapInfo files of middle-age.chr11.hapInfo.txt
grep chr11:110910907-110910951 /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/by_chrosomes/middle-age.chr11.hapInfo.txt
grep chr11:110910907-110910951  /home/shg047/monod/hap/wgbs/All_chromosomes_combined/WB_middle-age.all_chrs.hapInfo.txt

Latest revision as of 01:03, 23 October 2015


Compare methylation haplotype region with Hic Data[edit]

  • liftover epigenetic annotation from hg18 to hg19
./liftOver Hic.topological.domain.hESC.hg18.bed hg18ToHg19.over.chain Hic.topological.domain.hESC.hg19.bed tmp
./liftOver Hic.topological.domain.IMR90.hg18.bed  hg18ToHg19.over.chain Hic.topological.domain.IMR90.hg19.bed tmp
./liftOver Hic.boundary.IMR90.hg18.bed hg18ToHg19.over.chain Hic.boundary.IMR90.hg19.bed tmp
./liftOver Hic.boundary.hESC.hg18.bed hg18ToHg19.over.chain Hic.boundary.hESC.hg19.bed tmp
./liftOver Hic.common.boundary.hESC.IMR90.hg18.bed hg18ToHg19.over.chain Hic.common.boundary.hESC.IMR90.hg19.bed tmp
/home/sguo/monod/phase2/high.gsi.genome.cor.txt


Compare the cluster analysis with raw methylation signal[edit]

Achieve raw methylFreq files[edit]

  • I found the overlapped CpG sites between methylation haplotype and raw methylFreq (depth>5) was only 49. The reason when we calculate the methylation haplotype we did not get rid of low coverage reads. Therefore, I need collect the raw methylation methylFreq file and merage them again without low coverage reads discarding.
  • After discussing with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)
  • 651 CpG sites were found overlapped with 180 high GSI methylation haplotype regions. among them, 35 sites were found have more than 30% missing value and then were filtered in the further analysis.
  • the heatmap based on raw methylation signals were as the following(right). File:Heatmap.RawSignal.High.GSI.R.txt

File:GSI.RRBS.BSPP.WGBS.RawSignal.png

Comare MHL and Average methylation level[edit]

  • Bam to methyhaplotype
  • I found a problem, I do not know why non-CG would occur in methyhplot and why position would occur multiple time. You can try the following command:
grep chr6:53658269-53659397 /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/BSPP/mld_block_stringent_hapInfo/NC-23.WGBS_BSPP.mld_blocks_r2-0.5.hapInfo.txt


cd /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_stringent_hapInfo 
head 6-P-10.mld_blocks_r2-0.5.hapInfo.txt
chr10:100027865-100027869    TTT    2    100027865,100027867,100027869
chr10:100027897-100027992    TTTTT    17    100027957,100027961,100027981,100027988,100027992
chr10:100027897-100027992    GTTTT    1    100027927,100027930,100027938,100027944,100027957
chr10:100027897-100027992    TTTTTTTTT    15 100027908,100027918,100027922,100027925,100027927,100027930,100027938,100027944,100027957
chr10:100027897-100027992    TTT    2    100027897,100027899,100027908
chr10:100174838-100174961    TTT    2    100174838,100174852,100174875
chr10:100227297-100227560    TTTTT    10    100227438,100227445,100227449,100227466,100227488
chr10:100227297-100227560    TCTCT    1    100227438,100227445,100227449,100227466,100227488
chr10:100227297-100227560    TTTT    4    100227445,100227449,100227466,100227488
chr10:100227297-100227560    TTTTC    1    100227438,100227445,100227449,100227466,100227488
cd /media/Ext12T/DD_Ext12T/RRBS_MONOD/Bam_Merged/ 
samtools view 6-P-10.merged.bam chr10:100027865-100027869
cd /media/Ext12T/DD_Ext12T/RRBS_MONOD/Bam_Merged/ 
samtools view 6-P-1.merged.bam chr10:101089382-101089519 | less -S
cd /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_stringent_hapInfo 
head

Update new MHL[edit]

Code and Data[edit]

Code: File:Get methHap load matrix 01Oct2015.txt
All WGBS data: /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_Oct2015.txt
All RRBS data:/home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_Oct2015.txt
All WGBS-SeqCap data: /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_Oct2015.txt
  • methylation block regions (bed files for each chrosome and complete regions)
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr*.mld_blocks_r2-0.5.bed
  • specific loop in the pbs script
cd /oasis/tscc/scratch/k4zhang/MONOD/hESC_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr2.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/BAMfiles/methylC-seq_h1_r2.chr2.rmdup.bam > methylC-seq_h1_r2.chr2.hapInfo.txt
cd /oasis/tscc/scratch/k4zhang/MONOD/Ecker_Tissue_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr10.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/BAMfiles/STL001BL-01.chr10.sorted.clipped.bam > STL001BL-01.chr10.hapInfo.txt
cd /oasis/tscc/scratch/k4zhang/MONOD/N37_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chrX.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/BAMfiles/Indx22.chrX.rmdup.bam > N37-Stomach.chrX.hapInfo.txt
cd /oasis/tscc/scratch/k4zhang/MONOD/tumor_WGBS
/home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr8.mld_blocks_r2-0.5.bed  /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/HCT116.chr8.sorted.clipped.bam > HCT116.chr8.hapInfo.txt
  • the summarized samples are as the following:
/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr1.mld_blocks_r2-0.5.bed
/home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/N37_10_tissue_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/tumor_WGBS_sample_info_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/H1ESC_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/RRBS_merge/1407_RRBS_merbed_sampleInfo__WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/SeqCap/WGBS_SeqCap_plasma_sample_info.txt
/home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/TSCC_whole_blood_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/Ecker_Tissue_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt
/home/k4zhang/my_oasis_tscc/MONOD/WGBS_BSPP/WGBS_BSPP_sample_info.txt    # remember to delete \n before use
cp /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr1.mld_blocks_r2-0.5.bed /home/shg047/monod/haplo 
cp /home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/N37_10_tissue_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo 
cp /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/tumor_WGBS_sample_info_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/H1ESC_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/RRBS_merge/1407_RRBS_merbed_sampleInfo__WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/SeqCap/WGBS_SeqCap_plasma_sample_info.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/Ecker_Tissue_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/TSCC_whole_blood_WGBS_sampleInfo_WGBS-pooled-mld-blocks.txt /home/shg047/monod/haplo
cp /home/k4zhang/my_oasis_tscc/MONOD/WGBS_BSPP/WGBS_BSPP_sample_info.txt /home/shg047/monod/haplo
perl -p -i -e 's/MONOD\n/MONOD/g' WGBS_BSPP_sample_info.txt


methyhaplotype to matrix[edit]

  • transfer haplotype result (per chrosome per sample) to genome miner
  • methylation haplotype load (mhl) matrix
cp /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_combined/WGBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/
cp /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015/RRBS_methHap_load_matrix_Oct2015.txt /home/shg047/monod/oct/data/
cp /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/SeqCap/mld_blocks_July2015/WGBS_SeqCap_methHap_load_matrix_Oct2015.txt  /home/shg047/monod/oct/data/
  • extract absolute methylation levels within above regions(one value in each regions)
  • Bam files: ESC, Ecker, N37, age, Plasma were in the TSCC center
/home/k4zhang/my_oasis_tscc/MONOD/hESC_WGBS/BAMfiles/
/home/k4zhang/my_oasis_tscc/MONOD/Ecker_Tissue_WGBS/BAMfiles
/home/k4zhang/my_oasis_tscc/MONOD/N37_WGBS/BAMfiles
/home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/
/home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/
  • # chr17:16955467-16955609 in Colon_primary_tumor.chr17.sorted.clipped.bam
samtools tview -p chr17:16955467 /home/k4zhang/my_oasis_tscc/MONOD/tumor_WGBS/BAMfiles/Colon_primary_tumor.chr17.sorted.clipped.bam  /home/shg047/db/hg19.fa
  • # chr11:110910907-110910951 in middle-age.chr11.rmdup.bam
samtools tview -p chr11:110910907 /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/middle-age.chr11.rmdup.bam /home/shg047/db/hg19.fa
  • # grep chr11:110910907-110910951 in hapInfo files of middle-age.chr11.hapInfo.txt
grep chr11:110910907-110910951 /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/by_chrosomes/middle-age.chr11.hapInfo.txt
grep chr11:110910907-110910951  /home/shg047/monod/hap/wgbs/All_chromosomes_combined/WB_middle-age.all_chrs.hapInfo.txt