Kun:LabNotes/MONOD/2015-7-6

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Data analysis: re-defining bins based on methylation haplotype blocks

  • I have previously defined a set of methylation LD blocks based on the N37 and whole-blood WGBS data, plus tumor RRBS data:Kun:LabNotes/MONOD/2015-3-11.
  • Since several WGBS data sets have been published lately, I decided to repeat this using all WGBS data, in order to be as unbiased as possible.
  • The list of WGBS data sets included are (Dinh did all the mapping and gave me the mapped bam files):
    • Whole blood WGBS data (REF);
    • Our internal N37 WGBS data (ten tissues): /media/LTS_33T/WGBS_LTS33/Hg19/Noi_N37_WGBS/BAMfiles
    • WGBS data from H1 ESCs and differentiated cells (REF): /media/LTS_33T/WGBS_LTS33/Hg19/Xie2013/Re-map/BAMfiles
    • WGBS data from human adult tissues (Salk, REF): /media/TmpStore2/Dinh_Store2/Tissues_WGBS_Ecker/BAMfiles
    • WGBS data from a cancer cell line and a colon cancer tumor tissue (REF): /media/TmpStore2/Dinh_Store2/Tumor_WGBS/BAMfiles
  • I still use the same "mappable bins" to generate the initial hapInfo files for mld_block partitioning. This was done on TSCC since there are so many files to process.
    • Transfer bam files to TSCC.
    • Create a "sampleInfo" file to each data set.
    • Create job files and submit them to the queue.
 /home/k4zhang/my_oasis_tscc/MONOD/batch_bam2hapInfo2.pl  Media:H1ESC_WGBS_sampleInfo_mappable_bins.txt
 /home/k4zhang/my_oasis_tscc/MONOD/batch_bam2hapInfo2.pl  Media:Ecker-Tissue_WGBS_sampleInfo_mappable_bins.txt
 /home/k4zhang/my_oasis_tscc/MONOD/batch_bam2hapInfo2.pl  Media:N37_10_tissue_pool_WGBS_sampleInfo_mappable_bins.txt
 /home/k4zhang/my_oasis_tscc/MONOD/batch_bam2hapInfo2.pl  Media:whole_blood_WGBS_sampleInfo_mappable_bins.txt
 /home/k4zhang/my_oasis_tscc/MONOD/batch_bam2hapInfo2.pl  Media:tumor_WGBS_sampleInfo_mappable_bins.txt
    • Transfer all hapInfo files to genome-miner, merge and call mld_blocks.
 ./merge_all_WGBS_hapInfo_by_chr.pl
    • Transfer the bed files to TSCC, and generate all hapInfo files for the mld_blocks.