下载基因组注释gtf文件和下载参考基因组序列

下载GTF注释文件

对NCBI：

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GFF/ref_GRCh38.p7_top_level.gff3.gz          ## hg38
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/GFF/ref_GRCh37.p5_top_level.gff3.gz    ## hg19

对于ensembl：

wget ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.90.gtf.gz## hg38

wget ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz## hg19

变换中间的release就可以拿到所有版本信息：ftp://ftp.ensembl.org/pub/

对于UCSC

需要选择一系列参数：

http://genome.ucsc.edu/cgi-bin/hgTables

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:

clade: Mammal

genome: Human

assembly: Feb. 2009 (GRCh37/hg19)

group: Genes and Gene Predictions

track: UCSC Genes

table: knownGene

region: Select "genome" for the entire genome.

output format: GTF - gene transfer format

output file: enter a file name to save your results to a file, or leave blank to display results in the browser

3. Click 'get output'.

下载参考基因组序列

UCSC里面下载：

wegt http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz ##hg19
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/chromFa.tar.gz ##hg38

tar -zxvf chromFa.tar.gz

cd chroms

cat *.fa >hg19.fa

##hg38同样处理

NCBI:建议用迅雷或ncbi官网提供的下载器下载速度更快

##hg19：

for i in $(seq 1 22) X Y M;

do wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/Assembled_chromosomes/seq/hs_ref_GRCh37.p5_chr${i}.fa.gz; 

gzip -d hs_ref_GRCh37.p5_chr${i}.fa.gz;

cat hs_ref_GRCh37.p5_chr${i}.fa.gz >>hg19.fa;

sleep 10s;

done;

##hg38 ：

同理，只要找到下载地址，改动一下即可。

### ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/Assembled_chromosomes/seq/hs_ref_GRCh38.p7_chr${i}.fa.gz