GRCh38基因组和注释文件探究

ensembl/release91:

cat Homo_sapiens.GRCh38.91.gtf | grep -v "#" | cut -f9 | cut -f1,3,6,8 -d\; | grep gene_biotype | sed -e 's/\"//g' | sed -e 's/\;//g' | cut -f2,6,8 -d" " | sort | uniq > GRCh38.feature.info

ENSG00000000003 TSPAN6 protein_coding

ENSG00000000005 TNMD protein_coding

ENSG00000000419 DPM1 protein_coding

ENSG00000000457 SCYL3 protein_coding

ENSG00000000460 C1orf112 protein_coding

ENSG00000000938 FGR protein_coding

ENSG00000000971 CFH protein_coding

ENSG00000001036 FUCA2 protein_coding

ENSG00000001084 GCLC protein_coding

ENSG00000001167 NFYA protein_coding

ENSG00000001460 STPG1 protein_coding

ENSG00000001461 NIPAL3 protein_coding

ENSG00000001497 LAS1L protein_coding

ENSG00000001561 ENPP4 protein_coding

ENSG00000001617 SEMA3F protein_coding

ENSG00000001626 CFTR protein_coding

ENSG00000001629 ANKIB1 protein_coding

ENSG00000001630 CYP51A1 protein_coding

ENSG00000001631 KRIT1 protein_coding

ENSG00000002016 RAD52 protein_coding

ENSG00000002079 MYH16 transcribed_unitary_pseudogene

ENSG00000002330 BAD protein_coding

ENSG00000002549 LAP3 protein_coding

ENSG00000002586 CD99 protein_coding

ENSG00000002587 HS3ST1 protein_coding

ENSG00000002726 AOC1 protein_coding

ENSG00000002745 WNT16 protein_coding

ENSG00000002746 HECW1 protein_coding

ENSG00000002822 MAD1L1 protein_coding

ENSG00000002834 LASP1 protein_coding

ENSG00000002919 SNX11 protein_coding

ENSG00000002933 TMEM176A protein_coding

ENSG00000003056 M6PR protein_coding

ENSG00000003096 KLHL13 protein_coding

ENSG00000003137 CYP26B1 protein_coding

58302个ENSG id

56655个gene name（为什么有将近两千个是重复）

46种类型：

31 3prime_overlapping_ncRNA

   5517 antisense_RNA

     19 bidirectional_promoter_lncRNA

     14 IG_C_gene

      9 IG_C_pseudogene

     37 IG_D_gene

     18 IG_J_gene

      3 IG_J_pseudogene

      1 IG_pseudogene

    144 IG_V_gene

    188 IG_V_pseudogene

   7493 lincRNA

      1 macro_lncRNA

   1879 miRNA

   2221 misc_RNA

      2 Mt_rRNA

     22 Mt_tRNA

      3 non_coding

     63 polymorphic_pseudogene

  10235 processed_pseudogene

    543 processed_transcript

  19847 protein_coding

     22 pseudogene

      8 ribozyme

    549 rRNA

     49 scaRNA

      1 scRNA

    904 sense_intronic

    189 sense_overlapping

    943 snoRNA

   1909 snRNA

      5 sRNA

   1066 TEC

    462 transcribed_processed_pseudogene

    111 transcribed_unitary_pseudogene

    828 transcribed_unprocessed_pseudogene

      2 translated_processed_pseudogene

      6 TR_C_gene

      4 TR_D_gene

     79 TR_J_gene

      4 TR_J_pseudogene

    108 TR_V_gene

     30 TR_V_pseudogene

     95 unitary_pseudogene

   2637 unprocessed_pseudogene

      1 vaultRNA

GENCODE的注释gtf文件：　　

##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74)

##provider: GENCODE

##contact: gencode@sanger.ac.uk

##format: gtf

##date: 2013-12-05

chr1    HAVANA  gene    11869   14412   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";

chr1    HAVANA  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

chr1    HAVANA  exon    11869   12227   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

chr1    HAVANA  exon    12613   12721   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

chr1    HAVANA  exon    13221   14409   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

ensembl

#!genome-build GRCh38.p10

#!genome-version GRCh38

#!genome-date 2013-12

#!genome-build-accession NCBI:GCA_000001405.25

#!genebuild-last-updated 2017-06

1       havana  gene    11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";

1       havana  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype"processed_transcript"; tag "basic"; transcript_support_level "1";

1       havana  exon    11869   12227   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";

1       havana  exon    12613   12721   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";

1       havana  exon    13221   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";

1       havana  transcript      12010   13670   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype"transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";

问题：

1. 为什么用gencode的注释文件做表达定量会出问题？

2. 不同的release之间有什么区别？

3. 不同来源的注释区别在哪里？

GRCh38基因组和注释文件探究的更多相关文章

关于注释【code templates】，如何导入本地注释文件
关于如何在eclipse.myeclipse导入本地注释文件 [xxx.xml] 请看操作方式下面是code templates文件的内容注意把文件中的 @@@@@@@@@@@@@@@ ...
关于基因组注释文件GTF的解释
GTF文件的全称是gene transfer format,主要是对染色体上的基因进行标注.怎么理解呢,其实所谓的基因名,基因座等,都只是后来人们给一段DNA序列起的名字而已,还原到细胞中就是细胞核里 ...
【转】ubuntu中没有/etc/inittab文件探究
原文网址:http://blog.csdn.net/gavinr/article/details/6584582 linux 启动时第一个进程是/sbin/init,其主要功能就是软件执行环境,包括系 ...
如何用cufflinks 拼出一个理想的注释文件
后记: cufflinks安装: 下载安装包, 不要下载source code ,直接下载binary. Source code Linux x86_64 binary http://cu ...
HTTP上传文件探究
通常情况下,我们想在网页上上传一个文件的时候,会采用<input type="file">标签,但是你有没有想过,为什么通过这样一个标签,服务器端就能获取到文件数据呢? ...
ubuntu12.10中没有/etc/inittab文件探究
1. 我们首先来看一下Linux系统开机启动过程: Ubuntu是Linux系统的衍生系统,其开机启动过程与上图相差不大,但是随着系统的不断发展,终究还是有不同的地方,下面,我们来了解一下Ubuntu ...
初步了解hg19注释文件的内容 | gtf
hg19有哪些染色体? chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 c ...
idea 注释文件和方法注释
类注释: 如下图所示
[转] c++加载外部库文件探究
首先介绍:用#import导入dll和用#pragma comment导入lib还有在程序中LoadLibrary加载dll有什么区别 (1) #import导入的dll是com组建的dll,主要用来 ...

随机推荐

VC++ 判断一个文件是不是快捷方式
转载:https://bbs.csdn.net/topics/34999 #include <iostream> #include <Shlobj.h> #include &l ...
EGIT
https://jingyan.baidu.com/article/64d05a0262f013de55f73bcc.html
Download and Installation of Kibana
下载以及安装 https://www.elastic.co/downloads/kibana 1.Download and unzip Kibana 2. Open config/kibana.yml ...
Asp.Net 之 DropDownList的使用
这里不细说,直接上案例 <td style="width: 30px;" align="right"> 年月: </td> <td ...
BZOJ 4399 魔法少女LJJ（线段树合并）
题意 https://www.lydsy.com/JudgeOnline/problem.php?id=4399 思路码农题,需要一定代码功底.方法很暴力,先将权值离散,表示在线段树里储存的位置,每 ...
RequestMethod用法小结和注意事项
本文为博主原创,未经允许不得转载: RequestMethod为在@RequestMapping注解中使用的一个属性,用来标识请求的方法类型,可参考@RequestMapping源码: @Target ...
用spring tool suite插件创建spring boot项目时报An internal error occurred during: "Building UI model". com/google/common/
本文为博主原创,未经允许不得转载在用spring tool suite创建spring boot项目时,报一下异常: 查阅很多资料之后发现是因为装的spring tool suite的版本与ecli ...
js仿ppt，在线演示文档：Impress.js
(附件) Impress.js是一款基于css3转换和过渡.工作于现代浏览器(Google Chrome或Safari (或 Firefox 10 或 IE10)).并受prezi.com的理念启发 ...
python学习 day011打卡迭代器
本节的主要内容: 1.函数名的使用以及第一类对象 2.闭包 3.迭代器一.函数名的运用. 函数名是一个变量,但它是一个特殊的变量,与括号配合可以执行函数的变量. 1.函数名的内存地址 def fun ...
Md5混淆因子
package cn.springmvc.utils;import org.apache.commons.codec.digest.DigestUtils;import org.apache.comm ...

GRCh38基因组和注释文件探究

GRCh38基因组和注释文件探究的更多相关文章

随机推荐

热门专题