piranha 适用于CLIP-Seq 与 RIP-Seq 的 peak caller

最新推荐文章于 2024-08-21 08:33:22 发布

菠萝西斯

最新推荐文章于 2024-08-21 08:33:22 发布

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本文链接：https://blog.csdn.net/u013429737/article/details/117223962

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文章目录

前言: CLIP-Seq 与 RIP-Seq
一、piranha 简介
二、piranha 使用

前言: CLIP-Seq 与 RIP-Seq

简单的说，是RNA版本的ChIP-seq，CLIP-Seq 全称crosslinking-immunprecipitation and high-throughput sequencing，RIP-Seq 全称 RNA Binding Protein Immunoprecipitation and high-throughput sequencing。名字里说得很明确了，前者有一个紫外交联的步骤，后者没有，靠RNA结合蛋白免疫沉淀富集RNA。CLIP-Seq 与 RIP-Seq 都是用来测蛋白与RNA互做的，所以peak caller 是数据分析不可缺少的一部分。

一、piranha 简介

piranha, 南加州大学的Philip J. Uren 大神作品。一句话概括 Piranha is a peak-caller for CLIP- and RIP-seq data。

                    _____  _                 _            
                   |  __ \(_)               | |           
                   | |__) |_ _ __ __ _ _ __ | |__   __ _  
                   |  ___/| | '__/ _` | '_ \| '_ \ / _` | 
                   | |    | | | | (_| | | | | | | | (_| | 
                   |_|    |_|_|  \__,_|_| |_|_| |_|\__,_|
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                   *               V1.2.1               *
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二、piranha 使用

1. 安装

方便快捷的 conda https://anaconda.org/bioconda/piranha：

conda install -c bioconda piranha

在这里插入图片描述

2. 说明书

https://github.com/smithlabcode/piranha：

*********************************
Copyright and License Information
*******************************************************************************
Copyright (C) 2012
University of Southern California,
Philip J. Uren, Andrew D. Smith
  
Authors: Philip J. Uren, Emad Bahrami-Samani, Andrew D. Smith
  
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
  
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
  
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

This software package contains Google Test and BAMTools -- see their 
respective directories for copyright and license information for those 
packages. 


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