# MACS首先的工作是要确定一个模型,这个模型最关键的参数就是峰宽d,这个d就是bw(band width),而它的一半就是shiftsize $ macs2 callpeak -c controlFile.bam -t treatmentFile.bam -m 10 30 -p pvalue -f BAM -g gsize -B -n filename.preffix --outdir ChIP_seq/CallPeak 2>ChIP_seq/CallPeak...
安装成功后就可以直接使用MACS2进行peak calling了 代码语言:javascript 代码运行次数:0 运行 AI代码解释 # MACS首先的工作是要确定一个模型,这个模型最关键的参数就是峰宽d,这个d就是bw(band width),而它的一半就是shiftsize $ macs2 callpeak -c controlFile.bam -t treatmentFile.bam -m 10 30 -p pval...
callpeak-Options Variousoptionstoindicate/controlinput,output,peakmodellingandpeakcallingmacs2callpeakusage:macs2callpeak[-h]-tTFILE[TFILE...][-c[CFILE[CFILE...]]][-f{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}][-gGSIZE][--keep-dupKEEPDUPLICATES][--buffer-sizeBUFFER_SIZE...
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, ...
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}]...
12、UTOFF -call-summits,callpeak Options - Input,Input files arguments: -t TFILE TFILE ., -treatment TFILE TFILE . ChIP-seq treatment file. If multiple files are given as -t A B C, then they will all be read and combined. REQUIRED. -c CFILE CFILE ., -control CFILE CFILE . Co...
TypicallymillionsofreadspersamplePark,ics,2009ChIP-seq~200bp36-50bpControlsample:“Input”or“IgG”Input:sonicatedchromatinwithoutimmunoprecipitationIgG:“unspecific”IPMACS2Model-basedAnalysisofChIP--FarberCancerInstitute,BostonGenomeBiology2008,9:,developedandmaintainedbyTaoLiuat mandlineprogramstocallpeaksin...
macs3 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1 对于ATAC-seq双端数据的操作: macs3 callpeak -f BAMPE -t ATAC.bam -g hs -n test -B -q 0.01 -f是输入文件的格式,可以是BAM、BED,软件可以自动识别,但是需要注意自动识别是无法区分是PE还是SE,所以建议手动指定;...
macs2 callpeak 是macs2最主要的一个功能,能够利用bam文件寻找chip peak; macs2 callpeak 使用: # regular peak calling: macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01 # broad peakcalling:macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broa...
v1/README.rst MACS2–program(s)INPUTDATA:alignedsequencereads ChIPedsample“treat”Input/IgG“control”filterduprandsample callpeak predictd OUTPUTFILEs peaks.xlspeaks.narrowPeak summits.bedmodel.rmodel.pdf treat_pileup.bdgcontrol_lambda.bdg pileup refinepeaks bdgpeakcallbdgbroadcall ...