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.

library-type:fr-unstanded vs fisrt-stand vs second-stanrd的更多相关文章

  1. 1、创建一个JPA project(解决“at least one user library must be selected”问题)

    (注:本系列笔记是在学习尚硅谷JPA课程的时候写下的,结合课程内容和自我理解,方便自己以后进行复习) 一.在创建JPA之前看看什么是JPA 1.Java Persistence API:用于对象持久化 ...

  2. 深入理解shared pool共享池之library cache的library cache pin系列三

    关于library cache相关的LATCH非常多,名称差不多,我相信一些人对这些概念还是有些晕,我之前也有些晕,希望此文可以对这些概念有个更为清晰的理解,本文主要学习library cache p ...

  3. 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 ...

  4. V-rep学习笔记:Reflexxes Motion Library 1

    V-REP中集成了在线运动轨迹生成库Reflexxes Motion Library Type IV,目前Reflexxes公司已经被谷歌收购.(The Reflexxes Motion Librar ...

  5. .ner core InvalidOperationException: Cannot find compilation library location for package 'xxx' 和 SqlException: 'OFFSET' 附近有语法错误。 在 FETCH 语句中选项 NEXT 的用法无效。问题

    原文地址:传送门 1.InvalidOperationException: Cannot find compilation library location for package 'xxx'问题: ...

  6. FFmpeg源代码简单分析:configure

    ===================================================== FFmpeg的库函数源代码分析文章列表: [架构图] FFmpeg源代码结构图 - 解码 F ...

  7. Directional RNA-seq data -which parameters to choose?

    Directional RNA-seq data -which parameters to choose? REF: https://chipster.csc.fi/manual/library-ty ...

  8. Laravel图表扩展包推荐:Charts

     2016年11月15日 ·  2283次 ·  4条 ·  laravel,package,charts 介绍 在项目开发中,创建图表通常是一件痛苦的事情.因为你必须将数据转换为图表库支持的格式传输 ...

  9. PHP 5.6 编译安装选项说明

    `configure' configures this package to adapt to many kinds of systems. Usage: ./configure [OPTION].. ...

随机推荐

  1. 探讨电子商务新的商业模式O2O

    在当前的市场经济大环境下,电子商务成为了众 多中小企业用以开拓市场的主要工具,成为突破企业管理瓶颈的重要手段.必卖电子商务顾问认为,电子商务应该是是线上业务与线下业务的结合.对于从线下渠道 起家的传统 ...

  2. HTTPS请求 SSL证书验证

    import urllib2 url = "https://www.12306.cn/mormhweb/" headers = {"User-Agent": & ...

  3. 视频输出hdtv和sdtv

    SDTV和HDTV人们分别把它们叫标准清晰度数字电视和高清晰度数字电视,SDTV电视节目很早在欧洲就开始广播,如,DVB-S(卫星数字视频广播).DVB-C(有线数字视频广播).DVB-T(地面数字视 ...

  4. Redis特性和应用场景

    Redis特性 速度快 Redis使用标准C编写实现,而且将所有数据加载到内存中,所以速度非常快.官方提供的数据表明,在一个普通的Linux机器上,Redis读写速度分别达到81000/s和11000 ...

  5. 深入理解mockito

    深入理解mockito 初次使用 Mockito,能够感受到它的神奇,尤其是这样的语法: when(mockedList.get(0)).thenReturn("one") 指定当 ...

  6. 微信小程序结构分析

    1.Console页面:控制台信息页两个作用: (1)开发直接输入代码并且进行调试: (2)显示小程序的错误输出: 2.Sources页面:源文件调试信息页,用于显示当前项目的脚本文件. 3.Netw ...

  7. CodeIgniter框架——CI组件间信息流走向

    组件间信息流的走向图: 实线表示直接函数调用. 这些信息流可以从控制器到视图,也可以从控制器到类库或模型.(模型也能调用视图,但理论上这样做不合适.)相反方向就不能调用,如:视图不能调用控制器.然而, ...

  8. php后门管理工具weevely

    weevely是一款php后门管理工具,使用http头进行指令传输,功能强大.不过只支持php. weevely生成的服务器端php代码是经过了base64编码的,所以可以骗过主流的杀毒软件和IDS, ...

  9. SharePoint 2013 安装.net framework 4.5已经存在更高版本的解决方案

    请参考: https://support.microsoft.com/en-us/help/3087184/sharepoint-2013-or-project-server-2013-setup-e ...

  10. 巨蟒python全栈开发linux之centos4

    1.linux虚拟环境1-4 2.linux运行crm代码