基因/转录本/任意特征 表达定量工具之featureCounts使用方法 | 参数详解
featureCounts真的很厉害。
常见的参数（没什么好说的，毕竟是固定的）：
-a
-o
input_file1
-F
-t
-g
-Q
-T
关键是以下几个参数怎么设置：
-f # Perform read counting at feature level
-O # Assign reads to all their overlapping meta-features
-M # Multi-mapping reads will also be counted.
--primary # Count primary alignments only.
--ignoreDup # Ignore duplicate reads in read counting.
-s # Perform strand-specific read counting.
-p # If specified, fragments (or templates) will be counted instead of reads.
-B # Only count read pairs that have both ends aligned
-C # Do not count read pairs that have their two ends mapping
1. 什么时候需要在feature级别计数？
2. 是否要计多重比对？
3. 是否该只用最优比对？
When --primary is specified, the -M option will be ignored, meaning that a primary alignment will always be counted no matter the read is multi-mapped or not.
4. 是否要忽略重复reads？
5. pair-end模式下是否要用fragment计数？
For paired-end reads, you should count read pairs (fragments) rather than reads because counting fragments will give you more accurate counts. There are several reasons why you cannot get the fragment counts by simply dividing the counts you got from counting reads by two.
https://support.bioconductor.org/p/63824/
问题：
|| Total fragments : 706143 ||
|| Successfully assigned fragments : 71337 (10.1%) ||
|| Running time : 0.08 minutes ||
分配上的reads少得可怜，100%有问题！！！
因为我的unique比对率达到95%以上，怎么会这么少！！！
WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs).
最终查明：是注释文件的问题！！！正常是70%。
如果没有特别需求，STAR比对的时候就不要sort by coordinate了！！！sort一般都是为了建index
可以参考的链接：
不同参数的结果比较：
featureCounts -p -Q 10 -s 0 -T $cpu -a $gtf-o $out_dir/${sName}.all.counts.txt $out_dir/${sName}.hg19Aligned.out.bam
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required || || Features : 1199851 ||
|| Meta-features : 58302 ||
|| Chromosomes/contigs : 47 ||
|| || || Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Read re-ordering is performed. ||
|| ||
|| Total fragments : 419853 ||
|| Successfully assigned fragments : 306852 (73.1%) ||
|| Running time : 0.06 minutes ||
ssigned 306852
Unassigned_Unmapped 0
Unassigned_MappingQuality 0
Unassigned_Chimera 0
Unassigned_FragmentLength 0
Unassigned_Duplicate 0
Unassigned_MultiMapping 36280
Unassigned_Secondary 0
Unassigned_Nonjunction 0
Unassigned_NoFeatures 56950
Unassigned_Overlapping_Length 0
Unassigned_Ambiguity 19771
featureCounts -p -Q 10 -M -s 0 -T $cpu -a $gtf -o $out_dir/${sName}.all.counts.txt2 $out_dir/${sName}.hg19Aligned.out.bam
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\
|| || || Features : 1199851 ||
|| Meta-features : 58302 ||
|| Chromosomes/contigs : 47 ||
|| || || Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Read re-ordering is performed. ||
|| ||
|| Total fragments : 419853 ||
|| Successfully assigned fragments : 306852 (73.1%) ||
|| Running time : 0.05 minutes ||
Assigned 306852
Unassigned_Unmapped 0
Unassigned_MappingQuality 36280
Unassigned_Chimera 0
Unassigned_FragmentLength 0
Unassigned_Duplicate 0
Unassigned_MultiMapping 0
Unassigned_Secondary 0
Unassigned_Nonjunction 0
Unassigned_NoFeatures 56950
Unassigned_Overlapping_Length 0
Unassigned_Ambiguity 19771
featureCounts -p -Q 10 -B -s 0 -T $cpu -a $gtf -o $out_dir/${sName}.all.counts.txt3 $out_dir/${sName}.hg19Aligned.out.bam
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : required ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\
|| || || Features : 1199851 ||
|| Meta-features : 58302 ||
|| Chromosomes/contigs : 47 || || Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Read re-ordering is performed. ||
|| ||
|| Total fragments : 419853 ||
|| Successfully assigned fragments : 306500 (73.0%) ||
|| Running time : 0.05 minutes ||
Assigned 306500
Unassigned_Unmapped 656
Unassigned_MappingQuality 0
Unassigned_Chimera 0
Unassigned_FragmentLength 0
Unassigned_Duplicate 0
Unassigned_MultiMapping 36133
Unassigned_Secondary 0
Unassigned_Nonjunction 0
Unassigned_NoFeatures 56838
Unassigned_Overlapping_Length 0
Unassigned_Ambiguity 19726
featureCounts -p -Q 10 --ignoreDup -s 0 -T $cpu -a $gtf -o $out_dir/${sName}.all.counts.txt4 $out_dir/${sName}.hg19Aligned.out.bam
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| Duplicated Reads : ignored ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\
|| || || Features : 1199851 ||
|| Meta-features : 58302 ||
|| Chromosomes/contigs : 47 ||
|| || || Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Read re-ordering is performed. ||
|| ||
|| Total fragments : 419853 ||
|| Successfully assigned fragments : 306852 (73.1%) ||
|| Running time : 0.05 minutes ||
Assigned 306852
Unassigned_Unmapped 0
Unassigned_MappingQuality 0
Unassigned_Chimera 0
Unassigned_FragmentLength 0
Unassigned_Duplicate 0
Unassigned_MultiMapping 36280
Unassigned_Secondary 0
Unassigned_Nonjunction 0
Unassigned_NoFeatures 56950
Unassigned_Overlapping_Length 0
Unassigned_Ambiguity 19771
基因/转录本/任意特征 表达定量工具之featureCounts使用方法 | 参数详解的更多相关文章
- Python包管理工具setuptools之setup函数参数详解
**********************************************************对所学内容的简单汇总******************************** ...
- 抓包工具：tcpdump抓包命令详解
抓包工具:tcpdump抓包命令详解 简介: tcpdump全称:dump the traffic on a network,根据使用者的定义对网络上的数据包进行截获的包分析工具. tcpdump可以 ...
- 基于OpenCL的深度学习工具：AMD MLP及其使用详解
基于OpenCL的深度学习工具:AMD MLP及其使用详解 http://www.csdn.net/article/2015-08-05/2825390 发表于2015-08-05 16:33| 59 ...
- 『言善信』Fiddler工具 — 4、Fiddler面布局详解【工具栏】
目录 (一)工具栏详细介绍 1.第一组工具: 2.第二组工具: 3.第三组工具: 4.第四组工具: (二)工具栏使用说明 1.Fiddler修改代理端口: 2.过滤Tunnel to...443请求链 ...
- Mysql导入导出工具Mysqldump和Source命令用法详解
Mysql本身提供了命令行导出工具Mysqldump和Mysql Source导入命令进行SQL数据导入导出工作,通过Mysql命令行导出工具Mysqldump命令能够将Mysql数据导出为文本格式( ...
- [转]Mysql导入导出工具Mysqldump和Source命令用法详解
Mysql本身提供了命令行导出工具Mysqldump和Mysql Source导入命令进行SQL数据导入导出工作,通过Mysql命令行导出工具Mysqldump命令能够将Mysql数据导出为文本格式( ...
- 基于JDBC的跨平台数据库管理工具DbVisualizer安装步骤（图文详解）（博主推荐）
首先,关于跨平台数据库管理工具DbVisualizer是什么?这个不多说,大家自行去看. 这个工具可以自定义连接其他没有驱动的数据库. 公司的项目牵扯到的数据库有mysql,sqlserver,o ...
- Ubuntu14.04下Mongodb数据库可视化工具安装部署步骤（图文详解）（博主推荐）
不多说,直接上干货! 前期博客 Ubuntu14.04下Mongodb(离线安装方式|非apt-get)安装部署步骤(图文详解)(博主推荐) Ubuntu14.04下Mongodb官网安装部署步骤(图 ...
- Windows 运行chkdsk磁盘修复工具命令参数详解
chkdsk是Windows系统自带的磁盘修复工具,通常在电脑非正常关机之后再开机,系统就会自动调用chkdsk工具进行磁盘扫描和修复.同时,我们也可以在Windows系统中打开命令提示符,手动运行c ...
随机推荐
- VC++ 使用CreateProcess创建新进程
https://www.cnblogs.com/fancing/p/6477918.html #include <windows.h> #include <tchar.h> # ...
- 尚硅谷面试第一季-15Mysql什么时候建索引
课堂重点: MySQL的官方定义: 索引的优势: 索引的劣势: 那些情况下需要建立索引: 那些情况下不要建立索引: 何为过滤性:例如在数据库字段里,手机号/身份证号这些字段是过滤性好的字段,而性别则是 ...
- Bootstrap3基础 input-group glyphicon 输入框组与glyphicon图标
内容 参数 OS Windows 10 x64 browser Firefox 65.0.2 framework Bootstrap 3.3.7 editor ...
- java Swing小知识点
private JTextArea jta=new JTextArea(1,2); private ScrollPane sp=new ScrollPane(); private JPasswordF ...
- java后端学习路线
java基础-->java设计模式-->java数据结构与算法
- hdfoo站点开发笔记-2
httpd的目录的 Options: (里面的单词都是用的复数): Options Indexes FollowSymLinks 为了避免有些目录下没有生成deny.htm而显示列表, 可以直接给 / ...
- 洛谷1968美元汇率 dp
P1968 美元汇率 dp 题目描述 在以后的若干天里戴维将学习美元与德国马克的汇率.编写程序帮助戴维何时应买或卖马克或美元,使他从100美元开始,最后能获得最高可能的价值. 输入输出格式 输入格式: ...
- LOJ6283 数列分块入门7（分块）
pushdown的addtag[x]打成addtag[i],结果WA了一次 #include <cstdio> #include <algorithm> #include &l ...
- 题解——洛谷P2734 游戏A Game 题解（区间DP）
题面 题目背景 有如下一个双人游戏:N(2 <= N <= 100)个正整数的序列放在一个游戏平台上,游戏由玩家1开始,两人轮流从序列的任意一端取一个数,取数后该数字被去掉并累加到本玩家的 ...
- spring boot + session+redis解决session共享问题
自己没有亲自试过,不过看了下这个例子感觉靠谱,以后做了测试,在加以说明. PS:后期经验证,上面例子可行.我们平时存session里面的值,直接存在了redis里面了.