一、人類基因組有多大
- 參照UCSC提供的hg38版本，也是目前常用的人類參考基因組
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
chr size size2
1 chr1 248956422 249M
2 chr2 242193529 242M
3 chr3 198295559 198M
4 chr4 190214555 190M
5 chr5 181538259 182M
6 chr6 170805979 171M
7 chr7 159345973 159M
8 chrX 156040895 156M
9 chr8 145138636 145M
10 chr9 138394717 138M
11 chr11 135086622 135M
12 chr10 133797422 134M
13 chr12 133275309 133M
14 chr13 114364328 114M
15 chr14 107043718 107M
16 chr15 101991189 102M
17 chr16 90338345 90M
18 chr17 83257441 83M
19 chr18 80373285 80M
20 chr20 64444167 64M
21 chr19 58617616 59M
22 chrY 57227415 57M
23 chr22 50818468 51M
24 chr21 46709983 47M
25 SUM 3088269832 3088M
#未考慮M線粒體，其長度較短，為16569，16Kbp,
- 如上可看出染色體序號(hào)越靠前的，長度越大，范圍在50M~250M之間；
- 由于人為二倍體，所以基因組由60億個(gè)堿基組成；
- 參考基因組一般保存為純文本格式，即直接記錄“A”、“T”、“C”、“G”這樣的 ASCII 碼字符。
- 而1個(gè) ASCII 字符，大小是 1B，所以，如果按純文本保存 30億個(gè)字母(單鏈)，就是30億字母 = 3,000,000,000 B = 3 GB。
from NCBI
二、奇怪的染色體name(chrUn,random,alt)
- 同樣以UCSC里的hg38版本為例
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz
#提取染色體id
grep "^>" hg38.fa > chr.id
wc -l chr.id
#455 chr.id
head chr.id
####
>chr1
>chr10
>chr11
>chr11_KI270721v1_random
>chr12
>chr13
>chr14
>chr14_GL000009v2_random
>chr14_GL000225v1_random
>chr14_KI270722v1_random
- 如上發(fā)現(xiàn)，序列并不是只有25條(22+X+Y+M)，加起來共有455條。其它特殊的序列可分為三類。
-
在此之前需要簡單了解由最初的測(cè)序read數(shù)據(jù)組裝成基因組的染色體序列需要經(jīng)歷contigs與scaffolds兩個(gè)過程，如下圖所示。contigs是依靠read間的重疊拼接的序列(a few kbp long)，特點(diǎn)是不含有N堿基；scaffolds則主要依靠read pairs關(guān)系進(jìn)一步拼接contigs，特點(diǎn)是會(huì)產(chǎn)生N堿基(a few hundred kbp)；最終由scaffolds拼接成染色體序列。
read→contigs→scaffolds
read→chromosomes
2.1 Unlocalized scaffolds(*****random)
- a sequence found in an assembly that is associated with a specific chromosome but cannot be ordered or oriented on that chromosome.
- 簡單理解：知道這個(gè)scaffolds在哪條染色體上，但不知道其在染色體的具體位置及方向
- format: chr{chromosome number orname}_{sequence_accession}v{sequence_version}_random
grep "random" chr.id > chr.random
wc -l chr.random
#42 chr.random
head chr.random
###
>chr11_KI270721v1_random
>chr14_GL000009v2_random
>chr14_GL000225v1_random
>chr14_KI270722v1_random
>chr14_GL000194v1_random
>chr14_KI270723v1_random
>chr14_KI270724v1_random
>chr14_KI270725v1_random
>chr14_KI270726v1_random
2.2 Unplaced scaffolds(chrUn******)
- a sequence found in an assembly that is not associated with any chromosome.
- 簡單理解：不知道這條scaffolds的所屬染色體信息
- format: chrUn_{sequence_accession}v{sequence_version}
grep "chrUn" chr.id > chr.chrUn
wc -l chr.chrUn
#127 chr.chrUn
head chr.chrUn
###
>chrUn_KI270302v1
>chrUn_KI270304v1
>chrUn_KI270303v1
>chrUn_KI270305v1
>chrUn_KI270322v1
>chrUn_KI270320v1
>chrUn_KI270310v1
>chrUn_KI270316v1
>chrUn_KI270315v1
>chrUn_KI270312v1
2.3 Alternate loci scaffolds(*****alt)
- a scaffold that provides an alternate representation of a locus found in the primary assembly. These sequences do not represent a complete chromosome sequence although there is no hard limit on the size of the alternate locus; currently these are less than 1 Mb. These could either be NOVEL patch sequences, added through patch releases, or present in the initial assembly release.
- 簡單理解：參考基因組存在的主要依據(jù)是人類99.9%的序列是一致的。但是會(huì)存在一些序列在不同人群中不一致。例如49%人群該基因組特定位置為序列A，而49%人群則為序列B，都是正常的。但拿其中一種作為參考基因組都可能不太合適，因此標(biāo)記出Alternate loci scaffolds。
- format: chr{chromosome number or name}_{sequence_accession}v{sequence_version}_alt
- Alternate loci scaffolds為hg38版本基因組新添類型Sequence，此前hg19版本還沒有。
grep "alt" chr.id > chr.alt
wc -l chr.alt
#261 chr.alt
head chr.alt
###
>chr1_KI270762v1_alt
>chr1_KI270766v1_alt
>chr1_KI270760v1_alt
>chr1_KI270765v1_alt
>chr1_GL383518v1_alt
>chr1_GL383519v1_alt
>chr1_GL383520v2_alt
>chr1_KI270764v1_alt
>chr1_KI270763v1_alt
>chr1_KI270759v1_alt
注意：以上具體的chromosome name均為ucsc的hg版本，與GRCh38略有差異，但基本也是這幾種類型sequence
三、編碼基因占比多少
- 在30億堿基基因組中，能夠編碼蛋白質(zhì)的基因總長度只占總長度的5%，而其中轉(zhuǎn)錄本exon單元總長度只占總長度的1.5%；
- 人類染色體共編碼2w~3w個(gè)蛋白基因，分布于不同染色體中。平均長度有10Kbp長度左右，而實(shí)際上基因的長度分布十分廣泛(from a few hundred bases to more than 2 million bases)
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.refGene.gtf.gz
awk '{print$1, $10}' hg38.refGene.gtf |sort -k 2|uniq|grep -v alt | grep -v random | grep -v alt | grep -v fix| sort -k 1 > chr.gene
cut -d" " -f 1 chr.gene | uniq -c
###
1113 chr10
1676 chr11
1392 chr12
632 chr13
946 chr14
1010 chr15
1146 chr16
1574 chr17
434 chr18
1791 chr19
2832 chr1
780 chr20
414 chr21
644 chr22
1817 chr2
1563 chr3
1088 chr4
1313 chr5
1453 chr6
1341 chr7
1029 chr8
1114 chr9
1 chrM
1157 chrX
143 chrY
四、下載參考基因組
-
目前常用的基因組版本為GRCh38/37，hg38/19，前者可通過NCBI/Ensembl下載，后者可通過UCSC網(wǎng)站下載。如下圖所示GRCh38可認(rèn)為等同于hg38，GRCh37可認(rèn)為等同于hg19。
human genome version - 以下載GRCh38/hg38為例，如下
4.1 NCBI
wget -c ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz
NCBI
4.2 ensembl
- ensembl的release-103版本可以認(rèn)為等于GRCh38
- https://asia.ensembl.org/Homo_sapiens/Info/Index
- http://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/
- https://www.ensembl.org/info/data/ftp/index.html 還包含有cDNA轉(zhuǎn)錄本序列
wget -c http://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
ensembl
4.3 UCSC
- http://hgdownload.soe.ucsc.edu/downloads.html
- http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
UCSC
五、更新ing~
- 如有錯(cuò)誤歡迎指正；
- 以及關(guān)于生信研究中人類參考基因組其它常見問題，也可評(píng)論區(qū)留言，讓我們一起弄明白，加油~
