Macs2操作手册与介绍.pptVIP

ChIP-seq analysis with MACS2Tips and tricks Sami Heikkinen, PhD Docent in Molecular Bioinformatics Institute of Biomedicine, UEF Schmidt et al, Methods, 2009 ChIP-Seq simplified Where? Park, Nat Rev Genetics, 2009 From binding to binding sites Typically millions of reads per sample Park, Nat Rev Genetics, 2009 ChIP-seq ~200 bp 36-50 bp Control sample: “Input” or “IgG” Input: sonicated chromatin without immunoprecipitation IgG: “unspecific” IP MACS2 Model-based Analysis of ChIP-Seq Original version published by Yong Zhang and Tao Liu from the lab of X. Shirley Liu at the Dana-Farber Cancer Institute, Boston Genome Biology 2008, 9:R137 now at version 0140616, developed and maintained by Tao Liu at/taoliu/MACS/ /taoliu/MACS/blob/macs_v1/README.rst Package of command line programs to call peaks in ChIP-seq data Much improved since v1.x!!! diffpeak bdgdiff bdgcmp bdgbroadcall MACS2 – program(s) peaks.narrowPeak callpeak summits.bed peaks.xls model.r model.pdf INPUT DATA: aligned sequence reads OUTPUT FILEs treat_pileup.bdg control_lambda.bdg refinepeaks refinepeak.bed randsample filterdup predictd pileup pileup.bdg bdgpeakcall OUTPUT callpeak - Options Various options to indicate/control input, output, peak modelling and peak calling macs2 callpeak usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]] [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE, BAMPE}] [-g GSIZE] [--keep-dup KEEPDUPLICATES] [--buffer-size BUFFER_SIZE] [--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE] [--trackline] [--SPMR] [-s TSIZE] [--bw BW] [-m MFOLD MFOLD] [--fix-bimodal] [--nomodel] [--shift SHIFT] [--extsize EXTSIZE] [-q QVALUE] [-p PVALUE] [--to-large] [--ratio RATIO] [--down-sample] [--seed SEED] [--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL] [--broad] [--broad-cutoff BROADCUTOFF] [--call-summits] -t/--treatment FILENAME This is the only REQUIRED parameter for MACS. Using MACS – connect to server Open the SSH client at