library-type:fr-unstanded vs fisrt-stand vs second-stanrd

建库时是否是链特异性建库。

Tophat2:

--library-type The default is unstranded (fr-unstranded). If either fr-firststrand or fr-secondstrand is specified, every read alignment will have an XS attribute tag as explained below. Consider supplying library type options below to select the correct RNA-seq protocol.
Library Type Examples Description
fr-unstranded Standard Illumina Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand.
fr-firststrand dUTP, NSR, NNSR Same as above except we enforce the rule that the right-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced.
fr-secondstrand Ligation, Standard SOLiD Same as above except we enforce the rule that the left-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced.

HISAT2:--rna-strandness <string>

Specify strand-specific information: the default is unstranded.
For single-end reads, use F or R. ‘F‘ means a read corresponds to a transcript. ‘R‘ means a read corresponds to the reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF.
With this option being used, every read alignment will have an XS attribute tag: ‘+‘ means a read belongs to a transcript on ‘+‘ strand of genome. ‘-‘ means a read belongs to a transcript on ‘-‘ strand of genome.

时间: 2024-11-05 01:02:22

library-type:fr-unstanded vs fisrt-stand vs second-stanrd的相关文章

.NetCore2.0引用DLL报System.InvalidOperationException: Can not find compilation library location for package &#39;XXX&#39;

.NET CORE 2.0 MVC项目引用类库出现:System.InvalidOperationException: Can not find compilation library location for package 'XXX' 临时解决如下(据说2.0.1会修复):在Startup.cs文件中:修改: public void ConfigureServices(IServiceCollection services) { var mvcBuilder = services.AddMv

ASP.NET CORE MVC 2.0 项目中引用第三方DLL报错的解决办法 - InvalidOperationException: Cannot find compilation library location for package

目前在学习ASP.NET CORE MVC中,今天看到微软在ASP.NET CORE MVC 2.0中又恢复了允许开发人员引用第三方DLL程序集的功能,感到甚是高兴!于是我急忙写了个Demo想试试,我的项目结构如下: 可以看到解决方案中就两个项目,AspNetCoreWebApp就是一个ASP.NET CORE MVC 2.0的项目,而MyNetCoreLib是一个.Net Core 2.0的类库项目,为了体现AspNetCoreWebApp是通过程序集来引用MyNetCoreLib的,我还在解

centos 7.2 Apache+mysql+php step by step备忘

1. 如何允许laravel程序执行sudo shell脚本? chmod u+w /etc/sudoers ; echo "apache ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers 再注释掉Defaults requiretty这行,否则会要求有tty才能运行!(TODO: 写shell实现自动化) chmod u-w /etc/sudoers2. OS: CentOS 7.2 x643. 安装zend server ce: (由于ze

[C++] String Basic

Namespace Declarations A using declaration let us use a name from a namespace without qualify the name with a namespace_name:: prefix. // using namespace::name using std::vector using std::string  A sperate using declaration is required for each name

scala-eclipse

windows下scala的eclipse开发环境 步骤: 1,下载并安装scala,最新版 Download Previous Versions | The Scala Programming Language http://www.scala-lang.org/download/all.html 2,eclipse开发环境搭建 先说结论:最简单的方法,下载Scala IDE for Eclipse官网提供的集成scala的eclipse. 下载页面: Download Scala IDE f

Functions

1 Local static variables Local static variables are not destroyed when the function ends; they are destroyed when the program terminates. 2. Function parameter list Parameter names are optional. However, there is no way to use an unnamed parameter. A

addddd

Virtual Files A virtual file com.intellij.openapi.vfs.VirtualFile is the IntelliJ Platform's representation of a file in a file system (VFS). Most commonly, a virtual file is a file in your local file system. However, the IntelliJ Platform supports m

Swift views and controls

A view displays content, whereas a control is used to modify it in some way. A control (UIControl) is a subclass of UIView. views can not have action. But Gesture recognizers can be used to add actions for the views. An image view isn’t a control, so

Python中怎样读取文本.txt格式的文件

截取部分内容如下: 10.235186 11.321997 10.122339 11.810993 9.190236 8.904943 9.306371 9.847394 8.330131 8.340352 怎样将数据转化为矩阵? 第一步使用open()函数打开文件: 1 >>> fileName='D://softwareTool/Python/python_exerciseCode/Chap13_PCA//testSet.txt '; 2 >>> fr=open(f