构建index所需的参考基因组以及各种版本的注释文件

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一、参考基因组

Mapping or Alignment，是测序分析中重要的步骤。笼统的说，这一步骤就是把reads贴到参考基因组或转录组构建的index上的过程。那么，构建index，必不可少的就是fasta格式的参考基因组与参考转录组。
UCSC，ensemble，NCBI，genecode是下载参考基因组的来源网站。
几个版本基因组的对应关系：

NCBI	Ensembl	UCSC
GRCh36	release_52	hg18
GRCh37	release_59/61/64/68/69/75	hg19
GRCh38	release_76/77/78/80/81/82（更新中）	hg38

【以下操作，都hg38（GRCh38）为例】

1. UCSC

UCSC 网址：http://genome.ucsc.edu/

主页中的download -> genome Data，选human，就可以按需下载各种参考基因组了，一般通过ftp实现这个需求。

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/

一般流程需要的参考基因组以及参考转录组都在这里
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

通过ftp下载参考基因组：

$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
--2021-05-10 08:07:34--  http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163
Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 983659424 (938M) [application/x-gzip]
Saving to: ‘hg38.fa.gz’

hg38.fa.gz                  100%[===========================================>] 938.09M  9.55MB/s    in 95s     

2021-05-10 08:09:11 (9.82 MB/s) - ‘hg38.fa.gz’ saved [983659424/983659424]

938 MB，大小没问题，解压缩，浏览一下：

$ gunzip hg38.fa.gz 
$ grep ">" hg38.fa 
>chr1
>chr10
>chr11
>chr11_KI270721v1_random
>chr12
>chr13
>chr14
>chr14_GL000009v2_random
>chr14_GL000225v1_random
>chr14_KI270722v1_random
>chr14_GL000194v1_random
>chr14_KI270723v1_random
>chr14_KI270724v1_random
>chr14_KI270725v1_random
>chr14_KI270726v1_random
>chr15
>chr15_KI270727v1_random
>chr16
>chr16_KI270728v1_random
>chr17
>chr17_GL000205v2_random
>chr17_KI270729v1_random
>chr17_KI270730v1_random
>chr18
>chr19

值得注意的是，来自于UCSC的fasta，以“chr1”，“chr2”的方式标注染色体，找gtf或者gff注释的时候，要对于用对应的“chr1”，“chr2”标注。

2. ensemble

ensemble http://asia.ensembl.org/index.html 亚洲镜像，人类直接点Human就行了，默认GRCh38.p13。

http://asia.ensembl.org/Homo_sapiens/Info/Index 页面一目了然，左边基因组文件fasta，右边注释文件gtf，齐活。

同样通过ftp实现下载
http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/

$ wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
--2021-05-10 08:42:35--  (try: 2)  http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 881211416 (840M), 749449533 (715M) remaining [application/octet-stream]
Saving to: ‘Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz’

Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz               100%[++++++++++++++++++++=======================================================================================================================>] 840.39M   250KB/s    in 52m 57s 

2021-05-10 09:35:33 (230 KB/s) - ‘Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz’ saved [881211416/881211416]

$ gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz 
$ grep ">" Homo_sapiens.GRCh38.dna.primary_assembly.fa 
>1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
>10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF
>11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF
>12 dna:chromosome chromosome:GRCh38:12:1:133275309:1 REF
>13 dna:chromosome chromosome:GRCh38:13:1:114364328:1 REF
>14 dna:chromosome chromosome:GRCh38:14:1:107043718:1 REF
>15 dna:chromosome chromosome:GRCh38:15:1:101991189:1 REF
>16 dna:chromosome chromosome:GRCh38:16:1:90338345:1 REF
>17 dna:chromosome chromosome:GRCh38:17:1:83257441:1 REF
>18 dna:chromosome chromosome:GRCh38:18:1:80373285:1 REF
>19 dna:chromosome chromosome:GRCh38:19:1:58617616:1 REF
>2 dna:chromosome chromosome:GRCh38:2:1:242193529:1 REF
>20 dna:chromosome chromosome:GRCh38:20:1:64444167:1 REF
>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF
>22 dna:chromosome chromosome:GRCh38:22:1:50818468:1 REF
>3 dna:chromosome chromosome:GRCh38:3:1:198295559:1 REF
>4 dna:chromosome chromosome:GRCh38:4:1:190214555:1 REF
>5 dna:chromosome chromosome:GRCh38:5:1:181538259:1 REF
>6 dna:chromosome chromosome:GRCh38:6:1:170805979:1 REF
>7 dna:chromosome chromosome:GRCh38:7:1:159345973:1 REF
>8 dna:chromosome chromosome:GRCh38:8:1