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Large-scale integration group final update

Large-scale integration group final update. Michael M. Hoffman University of Washington 20 July 2010. Participants. Jason Ernst, Jay Gertz, Ross Hardison, Scott Hansen, Michael Hoffman, Rich Humbert, Jim Kent, Anshul Kundaje, Ali Mortazavi, Tim Reddy, Bob Thurman, Steve Wilder.

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Large-scale integration group final update

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  1. Large-scale integration groupfinal update Michael M. Hoffman University of Washington 20 July 2010

  2. Participants Jason Ernst, Jay Gertz, Ross Hardison, Scott Hansen, Michael Hoffman, Rich Humbert, Jim Kent, Anshul Kundaje, Ali Mortazavi, Tim Reddy, Bob Thurman, Steve Wilder

  3. Round 7 track decisions • Signal generation and segmentation for K562 (including “K562b”) • Untreated cells only • Histone modifications, CTCF, Pol2, DNase, FAIRE, input (for included groups) • Remove flagged experiments with poor IDR values (AnshulKundaje) • Data generation for final paper freeze will include available BAMs (either from our remapping or what’s available on DCC). Hard freeze! • Segway: input included as segmentation track • ChromHMM: potentially use peak calls instead of signal

  4. Wiggler options(formerly tagAlign2rawSignal) • Smoothing mode: rectangular up to cross-correlation peak (mode) • Tukey kernel: ratio of constant width to full width = 0.75 (default) • No input normalization • Discard positions where maxTags < 25% extLen • Pooling replicates except Stam lab where we use replicate rank #1 • Stack elimination (most are in low-mappability regions) (PCR amplification artifacts): Z-score>6 • Two significant figures after decimal point

  5. Blacklist regions • Terry Furey’s excluded regions • ACRO1, ALR/Alpha, BSR/Beta, (CATTC)n, chrM, (GAATG)n, (GAGTG)n, HSATII, LSU-rRNA_Hsa, SSU-rRNA_Hsa, TAR1 • Anshul’s high island regions (determined manually from input, DNase, FAIRE across all cell lines—some are pericentromeric)

  6. High island region

  7. Mnemonic abbreviations • D: dead zone • CD: CTCF (distal) • E: enhancer • TSS: TSS • GS: gene start • GM: gene middle • GE: gene end • R: repressive • Ew: weak enhancer • Em: medium-strength enhancer • Es: strong enhancer • TSSw: weak TSS • TSSs: strong TSS • sTSSs: Segway strong TSS • cCD: ChromHMM CTCF (distal)

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