-t/--treatment FILENAME
This is the only REQUIRED parameter for MACS.
Using MACS – connect to server
• Open the SSH client
– at Win –> All programs –> SSH Secure shell –> Secure shell client
the lab of X. Shirley Liu at the Dana-Farber Cancer Institute, Boston
– Genome Biology 2008, 9:R137 – now at version 2.1.0.20140616, developed and maintained by Tao
• Usage tip: use up/down arrow keys to move in command history • ls
– “Quick connect”
• connection : intron.uef.fi • username : <your user ID> • password: <your password>
Hale Waihona Puke Unix 101• pwd
– show Present Working Directory
• cd
– Change Directory – e.g. ‘cd /home/work/public’ to get to the folder we use today (from wherever
you are) – or, to get back to your home directory: ‘cd $HOME’ – or, back one step ‘cd ..’, or two steps ‘cd ../../’
predictd
OUTPUT FILEs
peaks.xls peaks.narrowPeak
summits.bed model.r model.pdf
treat_pileup.bdg control_lambda.bdg
pileup
refinepeaks
bdgpeakcall bdgbroadcall
[-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]
Liu at https:///taoliu/MACS/ – https:///taoliu/MACS/blob/macs_v1/README.rst
• Package of command line programs to call peaks in ChIPseq data
• Much improved since v1.x!!!
MACS2 – program(s)
INPUT DATA: aligned sequence reads
ChIPed sample “treat”
Input/IgG “control”
filterdup randsample
callpeak
Park, Nat Rev Genetics, 2009
Schmidt et al, Methods, 2009
From binding to binding sites
ChIP-seq
Control sample: “Input” or “IgG” - Input: sonicated chromatin
ChIP-seq analysis with MACS2
Tips and tricks
Sami Heikkinen, PhD Docent in Molecular Bioinformatics
Institute of Biomedicine, UEF
ChIP-Seq simplified
Where?
bdgcmp bdgdiff diffpeak
pileup.bdg refinepeak.bed
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}]
without immunoprecipitation - IgG: “unspecific” IP
~200 bp
36-50 bp
Typically millions of reads per sample
Park, Nat Rev Genetics, 2009
MACS2
• Model-based Analysis of ChIP-Seq • Original version published by Yong Zhang and Tao Liu from