# 其实hisat2-buld在运行的时候也会自己寻找exons和splice_sites,但是先做的目的是为了提高运行效率 extract_exons.py gencode.v26lift37.annotation.sorted.gtf>hg19.exons.gtf&extract_splice_sites.py gencode.v26lift37.annotation.gtf>hg19.splice_sites.gtf 建立index, 必须选项是基因组所在文件路径和输出的...
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Code availability HISAT2 and HISAT-genotype are open-source software freely available at https://github.com/DaehwanKimLab/hisat2. The HISAT2 package includes programs and application programming interfaces for C++, Python and JAVA that rapidly retrieve genomic locations from repeat alignments for us...
Picardhttps://broadinstitute.github.io/picard/ RSeQChttp://rseqc.sourceforge.net/ Qualimaphttp://qualimap.bioinfo.cipf.es/ (1)对BAM文件进行统计分析 RSeQC的安装,需要先安装gcc;numpy;R;Python2.7,这里比较难装的就是numpy——可以直接利用anaconda安装 #启动python2.7环境$ source activate python2#安装num...
首先,分析RNAseq要对整个分析流程有个整体的了解: 参考https://tiramisutes.github.io/2018/12/04/ref-RNA-seq.html 详细介绍了主要用到的分析工具和流程。这里我主要介绍一下我常用的分析流程 拿到原始数据首先需要对文件完整性进行检查 md5sum file #输出的MD5和测序公司给的进行对比,一样则说明文件完整 #或者...
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Final word: Adding this code to your GitHub Repository This repository was built in place and then uploaded to the repository on GitHub. To do so in the https://shell.google.com environment we need to get install the interactive set of tools for GitHub obtainable from https://anaconda.org...
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