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+Xshell賬號(hào)：jxzhou密碼：jxzhou_110107Linux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安裝方法：Linux：wget-c/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh（任選其一）wget-c/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh（任選其一）Mac：curl-0/anaconda/miniconda/Miniconda3-1atest-Mac0sX-x86_64.shConda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方法一: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:$PATH'>>~/.bashrcsource~/.bashrcfastqc–h##檢驗(yàn)有沒有安裝成功以及查看使用方法方法二:condainstallfastqcRNA-Seq環(huán)境搭建RNA-Seq分析流程Trimmomatic：/p/bc3ad9379e3e安裝命令：mkdirTrimmomaticwget/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zipunzipTrimmomatic-0.38.zip##解壓就能用RNA-Seq環(huán)境搭建RNA-Seq分析流程HISAT2：/p/8875580ffe7e方法一:安裝命令：mkdirHISAT2wget/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zipunziphisat2-2.1.0-source.zipmake##編譯安裝hisat2–h方法二:condainstallhisat2RNA-Seq環(huán)境搭建RNA-Seq分析流程Samtools：/p/6b7a442d293f方法一:安裝命令：mkdirsamtoolswget-c/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2tarjxvfsamtools-1.9.tar.bz2./configure--prefix=/home/vip47/biosoft/samtools-1.9##編譯軟件安裝，這里需要絕對(duì)路徑make##編譯安裝makeinstallecho'exportLD_LIBRARY_PATH=/public/home/cding/software/libffi/libffi-3.3/lib64:$PATH'>>~/.bashrcsource~/.bashrcsamtools-h方法二:condainstallsamtoolsRNA-Seq環(huán)境搭建RNA-Seq分析流程HTSeq：/liujiaxin2018/p/17335939.html方法一: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)用目錄方法二/三: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方法一:安裝命令：mkdirBWAgitclone/lh3/bwa.git#下載cdbwa&&make#安裝echo'PATH=$PATH:/home/train/biosoft/bwa/'>>~/.bashrcsource~/.bashrcbwa–h方法二:condainstallbwaChIP-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_aiomsg方法一:mkdirdeepTools&&cddeepToolsgitclone/fidelram/deepToolscddeepTools/pythonsetup.pyinstall--user~/.local/bin/deeptools方法二:pipinstalldeeptoolscondainstalldeeptools1.1RNA-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CONTENTSHi-C環(huán)境搭建Hi-C分析流程HiC-Pro軟件鏈接：/nservant/HiC-ProHic-pro的安裝_hicpro安裝-CSDN博客博客中軟件使用參考：/p/9a1e1680bb7bHiC-Pro-i/raw_data-/Hi-C/out-cconfig-hicpro.txtHi-C環(huán)境搭建Hi-C分析流程HiC-Pro軟件鏈接：/nservant/HiC-ProHic-pro的安裝_hicpro安裝-CSDN博客博客中軟件使用參考：/p/9a1e1680bb7bHi-C環(huán)境搭建HiC-Pro安裝：1.下載并解壓安裝包：wget-c/nservant/HiC-Pro/archive/refs/tags/v3.1.0.tar.gztar-zxvfHiC-Pro-3.1.0.tar.gz2.創(chuàng)建虛擬環(huán)境condaenvcreate-fHiC-Pro-3.1.0/environment.yml-nnehic3.進(jìn)入HiC-Pro-3.1.0配置config-install.txtviconfig-install.txtHi-C環(huán)境搭建HiC-Pro安裝：4.執(zhí)行makeconfigure命令此時(shí)多了一個(gè)config-system.txtHi-C環(huán)境搭建HiC-Pro安裝：5.查看config-system.txt文件6.執(zhí)行make命令安裝成功Hi-C環(huán)境搭建HiC-Pro安裝：7.配置環(huán)境變量（退出虛擬環(huán)境）vi~/.bashrc任意路徑下輸入HiC-Pro，都會(huì)輸出使用信息ChIA-PET分析流程GitHub-GuoliangLi-HZAU/ChIA-PET_Tool數(shù)據(jù)下載數(shù)據(jù)來源：做實(shí)驗(yàn)、測(cè)序網(wǎng)上下載數(shù)據(jù)下載1.登錄NCBI網(wǎng)頁：/2.搜索GEO號(hào)3.找到測(cè)序數(shù)據(jù)測(cè)序數(shù)據(jù)下載4.點(diǎn)擊SRA號(hào)5.點(diǎn)擊SRR號(hào)測(cè)序數(shù)據(jù)下載6.點(diǎn)擊Dataaccess后，復(fù)制NCBI