[1] bedtools (https://github.com/arq5x/bedtools2) here is also bedtools (https://github.com/arq5x/bedtools2) getfasta. It uses Erik's code under the hood. $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ be…

转载来自: http://www.infocool.net/kb/PHP/201607/168683.html a 函数 说明 abs 绝对值 acos 反余弦 acosh 反双曲余弦 addcslashes 以 C 语言风格使用反斜线转义字符串中的字符 addslashes 使用反斜线引用字符串 apache_child_terminate 在本次请求结束后终止 apache 子进程 apache_getenv 获取 Apache subprocess_env 变量 apache_get_mo…

by Umer Zeeshan Ijaz The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to t…

http://gmod.org/wiki/MAKER_Tutorial 简单好用 identify repeats, to align ESTs and proteins to the genome, and to automatically synthesize these data into feature-rich gene annotations, including alternative splicing and UTRs, as well as attributes such as…

详细的使用说明:http://bedtools.readthedocs.org/en/latest/ Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genom…

Linux下可以直接用mail命令发送邮件,但是发件人是user@servername,如果机器没有外网的dns,其他人就无法回复.此时,有一个可以使用网络免费邮箱服务的邮件发送程序就比较重要了.msmtp就是这样的一个程序. 一.安装msmtp 1.下载源码包 cd /usr/local/src && wget https://nchc.dl.sourceforge.net/project/msmtp/msmtp/1.6.6/msmtp-1.6.6.tar.xz 2.编译安装 注意:由于…

一.引言 前一段在做一个csv的导入工具,最麻烦的部分就是对csv文件的解析,最后,老大提醒说是不是考虑的过于麻烦了,由于当时考虑到mysql是允许指定导出的csv文件的格式的,所以考虑到想要兼容这种方式,于是思路就麻烦了,考虑到一些特殊的符号,比如:数据中可能存在换行符,这样就无法按行读取了:所以,思路是读取一块数据,然后一个一个字符的解析数据:听了老大的提示,然后我就考虑是不是真的考虑麻烦了,实际环境中换行符处在数据中的情况是相当少见的,我就还从mysql入手,mysql导出csv是使用的语…

来源:STARmanual.pdf 来源:Calling variants in RNAseq PART0 准备工作 #STAR 安装前的依赖的工具 #Red Hat, CentOS, Fedora. sudo yum update sudo yum install make sudo yum install gcc-c++ sudo yum install glibc-static PART1 Quick start #STAR Basic workflow ###1. Generating…

转载: https://github.com/twbattaglia/RNAseq-workflow Introduction RNAseq is becoming the one of the most prominent methods for measuring celluar responses. Not only does RNAseq have the ability to analyze differences in gene expression between samples,…

DPKG commands There are two actions, they are dpkg-query and dpkg-deb. Install a package # sudo dpkg -i {package_name} # sudo dpkg -i skype-ubuntu-precise_4.2.0.11-1_i386.deb Remove a package # sudo dpkg -r {package_name} # sudo dpkg -r vlc Remove a…