下載GTF註釋檔案 對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 對於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

對於UCSC 需要選擇一系列引數： 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'. 下載參考基因組序列 UCSC裡面下載：
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同樣處理 NCBI:建議用迅雷或ncbi官網提供的下載器下載速度更快 ##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，只要找到下載地址，改動一下即可。 ###ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/Assembled_chromosomes/seq/hs_ref_GRCh38.p7_chr${i}.fa.gz