組學(xué)數(shù)據(jù)分析環(huán)境搭建

2025年4月16日1.1RNA-Seq數(shù)據(jù)分析環(huán)境搭建

1.2ChIP-Seq數(shù)據(jù)分析環(huán)境搭建

1.3Hi-C數(shù)據(jù)分析環(huán)境搭建

目錄CONTENTS1.1RNA-Seq數(shù)據(jù)分析環(huán)境搭建

1.2ChIP-Seq數(shù)據(jù)分析環(huán)境搭建

1.3Hi-C數(shù)據(jù)分析環(huán)境搭建

目錄CONTENTSLinux環(huán)境創(chuàng)建Windows電腦：Xftp+XshellMac電腦：FileZilla+Mac電腦終端Linux環(huán)境創(chuàng)建Windows電腦：Xftp+XshellLinux環(huán)境創(chuàng)建Windows電腦：Xftp+XshellLinux環(huán)境創(chuàng)建Mac電腦：FileZilla+Mac電腦終端ssh–p

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gtchen@42Conda環(huán)境搭建Conda是一個(gè)開源的包管理和環(huán)境管理工具，最初為Python設(shè)計(jì)，但支持多語言，用于解決依賴沖突和隔離開發(fā)環(huán)境。/p/edaa744ea47dConda安裝：Conda環(huán)境搭建用conda創(chuàng)建自己的環(huán)境：condacreate-npython2python=2#-n:設(shè)置新的環(huán)境的名字，設(shè)置自己的名字查看已安裝的環(huán)境condaenvlist啟動(dòng)condacondaactivate（可加某一個(gè)環(huán)境名字）退出conda環(huán)境condadeactivateRNA-Seq環(huán)境搭建RNA-Seq分析流程原始數(shù)據(jù)→FastQC質(zhì)量檢測(cè)→Trimmomatic過濾→HISAT2比對(duì)→Samtoolssam轉(zhuǎn)bam/取唯一/排序→HTSeq計(jì)數(shù)→DESeq2差異FastQC：/p/bc3ad9379e3eTrimmomatic：/p/bc3ad9379e3eHISAT2：/p/8875580ffe7eSamtools：/p/6b7a442d293fHTSeq：/liujiaxin2018/p/17335939.htmlRNA-Seq環(huán)境搭建RNA-Seq分析流程FastQC：/p/bc3ad9379e3e安裝命令：mkdirFastqcwgethttp://www.bioinformatics.Babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zipunzipfastqc_v0.11.7.zipchmod755fastqcecho'exportLD_LIBRARY_PATH=/public/home/cding/software/libffi/libffi-3.3/lib64:$PATH'>>~/.bashrcsource~/.bashrcfastqc–h##檢驗(yàn)有沒有安裝成功以及查看使用方法condainstallfastqcRNA-Seq環(huán)境搭建RNA-Seq分析流程Trimmomatic：/p/bc3ad9379e3e安裝命令：mkdirTrimmomaticwget/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zipunzipTrimmomatic-0.38.zip##解壓就能用RNA-Seq環(huán)境搭建RNA-Seq分析流程HISAT2：/p/8875580ffe7e安裝命令：mkdirHISAT2wget/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zipunziphisat2-2.1.0-source.zipmake##編譯安裝hisat2-hcondainstallhisat2unziphisat2-2.1.0-source.zip

RNA-Seq環(huán)境搭建RNA-Seq分析流程Samtools：/p/6b7a442d293f安裝命令：mkdirsamtoolswget-c/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2tarjxvfsamtools-1.9.tar.bz2./configure--prefix=/home/vip47/biosoft/samtools-1.9##編譯軟件安裝，這里需要絕對(duì)路徑make##編譯安裝makeinstallecho'exportLD_LIBRARY_PATH=/public/home/cding/software/libffi/libffi-3.3/lib64:$PATH'>>~/.bashrcsource~/.bashrcsamtools-hcondainstallsamtoolsunziphisat2-2.1.0-source.zip

RNA-Seq環(huán)境搭建RNA-Seq分析流程HTSeq：/liujiaxin2018/p/17335939.html安裝命令：mkdirHTSeqwget/packages/fd/94/b7c8c1dcb7a3c3dcbde66b8d29583df4fa0059d88cc3592f62d15ef539a2/HTSeq-0.9.1.tar.gztar-xzvfHTSeq-0.9.1.tar.gz##解壓cdHTSeq-0.9.1/pythonsetup.pybuildpythonsetup.pyinstall--user##安裝cd~/.local/bin/##進(jìn)入軟件可調(diào)用目錄pipinstallhtseqcondainstallhtseq1.1RNA-Seq數(shù)據(jù)分析環(huán)境搭建

1.2ChIP-Seq數(shù)據(jù)分析環(huán)境搭建

1.3Hi-C數(shù)據(jù)分析環(huán)境搭建

目錄CONTENTSChIP-Seq環(huán)境搭建ChIP-Seq分析流程原始數(shù)據(jù)→FastQC質(zhì)量檢測(cè)→Trimmomatic過濾→BWA-MEM比對(duì)→Samtools去重→質(zhì)量篩選→MACS2峰識(shí)別→deepTools格式轉(zhuǎn)換→IGV可視化BWA：/p/553c9fe387c1MAC2：/weixin_33805743/article/details/86230451deepTools：/p/ea7abe0464c1?tdsourcetag=s_pcqq_aiomsgChIP-Seq環(huán)境搭建ChIP-Seq分析流程BWA：/p/553c9fe387c1安裝命令：mkdirBWAgitclone/lh3/bwa.git#下載cdbwa&&make#安裝echo'PATH=$PATH:/home/train/biosoft/bwa/'>>~/.bashrcsource~/.bashrcbwa–hcondainstallbwaChIP-Seq環(huán)境搭建ChIP-Seq分析流程MAC2：/weixin_33805743/article/details/86230451pipinstallMACS2condainstallMACS2ChIP-Seq環(huán)境搭建ChIP-Seq分析流程deepTools：/p/ea7abe0464c1?tdsourcetag=s_pcqq_aiomsgmkdirdeepTools&&cddeepToolsgitclone/fidelram/deepToolscddeepTools/pythonsetup.pyinstall--user~/.local/bin/deeptoolspipinstalldeeptoolscondainstalldeeptools1.1RNA-Seq數(shù)據(jù)分析