6、RNA-Seq Analysis Pipeline
Created by Dhivya Arasappan, last modified by Dennis C Wylie on Nov 08, 2015
1. Quality Assessment
Quality of data assessed by FastQC; results of quality assessment will be evaluated prior to downstream analysis.
- Deliverables:
- reports generated by FastQC
- Tools used:
- FastQC: (Andrews 2010) used to generate quality summaries of data:
- Per base sequence quality report: useful for deciding if trimming necessary.
- Sequence duplication levels: evaluation of library complexity. Higher levels of sequence duplication may be expected for high coverage RNAseq data.
- Overrepresented sequences: evaluation of adapter contamination.
- FastQC: (Andrews 2010) used to generate quality summaries of data:
2. Fastq Preprocessing
Quality assessment used to decide if any preprocessing of the raw data is required and if so, preprocessing is performed.
- Deliverables:
- Trimmed/filtered fastq files.
- Tools Used:
- Fastx-toolkit: Used to preprocess fastq files.
- Fastq quality trimmer: Trimming reads based on quality.
- Fastq quality filter: Filtering reads based on quality.
- Cutadapt: Used to remove adaptor from reads.
- Fastx-toolkit: Used to preprocess fastq files.
3. Mapping
Mapping to genome reference performed using BWA-mem or Tophat.
- Deliverables:
- Mapping results, as bam files and mapping statistics.
- Tools Used:
- BWA-mem: (Li 2013) primary aligner used to generate read alignments.
- Tophat: (Kim 2011) aligner used to generate read alignments in a splice-aware manner and identify novel junctions.
- Samtools: (Li 2009) used to generate mapping statistics.
4. Gene/Transcript Counting
Counting the number of reads mapping to annotated intervals to obtain abundance of genes/transcripts.
- Deliverables:
- Raw gene/transcript counts
- Tools Used:
- HTSeq-count: (Anders 2014) used to count reads overlapping gene intervals.
5. DEG Identification
Normalization and statistical testing to identify differentially expressed genes.
- Deliverables:
- DEG Summary and master file containing fold changes and p values for every gene, MA Plots.
- Tools Used:
- DESeq2: (Love 2014) used to perform normalization and test for differential expression using the negative binomial distribution.
6、RNA-Seq Analysis Pipeline的更多相关文章
- RNA -seq
RNA -seq RNA-seq目的.用处::可以帮助我们了解,各种比较条件下,所有基因的表达情况的差异. 比如:正常组织和肿瘤组织的之间的差异:检测药物治疗前后,基因表达的差异:检测发育过程中,不同 ...
- RNA seq 两种计算基因表达量方法
两种RNA seq的基因表达量计算方法: 1. RPKM:http://www.plob.org/2011/10/24/294.html 2. RSEM:这个是TCGAdata中使用的.RSEM据说比 ...
- Power BI 与 Azure Analysis Services 的数据关联:1、建立 Azure Analysis Services服务
Power BI 与 Azure Analysis Services 的数据关联:1.建立 Azure Analysis Services服务
- xgene:之ROC曲线、ctDNA、small-RNA seq、甲基化seq、单细胞DNA, mRNA
灵敏度高 == 假阴性率低,即漏检率低,即有病人却没有发现出来的概率低. 用于判断:有一部分人患有一种疾病,某种检验方法可以在人群中检出多少个病人来. 特异性高 == 假阳性率低,即错把健康判定为病人 ...
- Scrapy框架——介绍、安装、命令行创建,启动、项目目录结构介绍、Spiders文件夹详解(包括去重规则)、Selectors解析页面、Items、pipelines(自定义pipeline)、下载中间件(Downloader Middleware)、爬虫中间件、信号
一 介绍 Scrapy一个开源和协作的框架,其最初是为了页面抓取 (更确切来说, 网络抓取 )所设计的,使用它可以以快速.简单.可扩展的方式从网站中提取所需的数据.但目前Scrapy的用途十分广泛,可 ...
- 7、RNAseq Downstream Analysis
Created by Dennis C Wylie, last modified on Jun 29, 2015 Machine learning methods (including cluster ...
- 五、Scrapy中Item Pipeline的用法
本文转载自以下链接: https://scrapy-chs.readthedocs.io/zh_CN/latest/topics/item-pipeline.html https://doc.scra ...
- 09、RNA降解图的计算过程
RNA降解是影响芯片质量的一个很重要的因素,因为RNA是从5’开始降解的,所以理论5’的荧光强度要低于3’.RNA降解曲线可以表现这种趋势. 以样品GSM286756.CEL和GSM286757.CE ...
- RNA测序相对基因表达芯片有什么优势?
RNA测序相对基因表达芯片有什么优势? RNA-Seq和基因表达芯片相比,哪种方法更有优势?关键看适用不适用.那么RNA-Seq适用哪些研究方向?是否您的研究?来跟随本文了解一下RNA测序相对基因表达 ...
随机推荐
- mini2440移植uboot 2014.04(四)
我修改的代码已经上传到github上,地址:https://github.com/qiaoyuguo/u-boot-2014.04-mini2440.git 参考文章: <mini2440移植u ...
- Linux Shell总结
Shell编程总结: 1.linux命令 2.位置变量 $0 $1 $# $? 3.条件测试 [ ] [[ ]] (( )) if case 4.循环for while 5.打印echo cat 6. ...
- 斐波那契 (Fibonacci)数列
尾递归会将本次方法的结果计算出来,直接传递给下个方法.效率很快. 一般的递归,在本次方法结果还没出来的时候,就调用了下次的递归, 而程序就要将部分的结果保存在内存中,直到后面的方法结束,再返回来计算. ...
- <a href
<%@ page language="java" contentType="text/html; charset=ISO-8859-1" pageEnco ...
- LINQ 学习路程 -- 查询例子
IList<Student> studentList = new List<Student>() { , StudentName = , StandardID = } , , ...
- wiredtiger存储引擎介绍——本质就是LSM,当然里面也可以包含btree和列存储
见:http://www.slideshare.net/profyclub_ru/4-understanding-and-tuning-wired-tiger-the-new-high-perform ...
- Java_注解_00_资源贴
1.Java注解教程:自定义注解示例,利用反射进行解析 2. (1)深入理解Java:注解(Annotation)基本概念 (2)深入理解Java:注解(Annotation)自定义注解入门 (3)深 ...
- OpenCV——径向模糊
参考来源: 学习OpenCV:滤镜系列(5)--径向模糊:缩放&旋转 // define head function #ifndef PS_ALGORITHM_H_INCLUDED #defi ...
- u盘安装ubuntu 12.04 server问题解决
问题: 使用UltraISO 9.5.3制作U盘启动盘,ISO文件使用ubuntu-12.04.2-server-i386.iso,ISO文件经过MD5验证是正确的. 将U盘查到计算机上,进bios选 ...
- 【LeetCode】033. Search in Rotated Sorted Array
题目: Suppose an array sorted in ascending order is rotated at some pivot unknown to you beforehand. ( ...