這里以小鼠為例子下載相應的注釋文件，基因組版本為mm10

• 下載refGene.txt.gz
  網(wǎng)址:http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/
  wget http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz
• 下載gene_info.gz文件
  網(wǎng)址：ftp://ftp.ncbi.nih.gov/gene/DATA/
  wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
• 使用寫好的腳本對下載文件進行處理，小鼠tax id 10090

less -S gene_info.gz | awk -F "\t" '{if($1=="10090") print $2"\t"$3"\t"$5}' >../mm10.IDless -S refGene.txt.g |awk -F "\t" '{print $2"\t"$13}' >mm10.nameperl gene.pl ../mm10.ID mm10.name mm10-id-geneperl turn.pl mm10-id-gene refGene.txt.gz Gene.bed.2 less Gene.bed.2 |sort -k 1,1 -k 2,2n > Gene.bed rm Gene.bed.2perl Gene2exon_intron.pl refGene.txt.gz sort -k 1,1 -k 2,2n exon.bed>Exon.bed sort -k 1,1 -k 2,2n intron.bed>Intron.bed rm exon.bed intron.bedperl get4Intergenic.pl Gene.bed 2000

• GO and KEGG

less -S /ldfssz1/ST_BIGDATA/USER/yueyao/12.Pro/04.RNASeq/gene2go.gz |grep "^10090" >mm10.go perl /ifs4/BC_PUB/biosoft/pipeline/RNA/RNA_RNAdenovo/RNA_RNAdenovo_2016a/Annotation/annot2goa.pl /ifs4/BC_PUB/biosoft/db/Pub/go/RNA/20171220/gene_ontology.1_2.obo mm10.annot /ldfssz1/ST_BIGDATA/USER/yueyao/16.Pipeline/chipseq_test/mmdatabase/GO/mm10 perl dealGOObo.pl -go /ifs4/BC_PUB/biosoft/db/Pub/go/RNA/20171220/gene_ontology.1_2.obo -prefix go les /ifs4/BC_PUB/biosoft/db/Pub/kegg/RNA/84.0/animal.id.annot.xls |grep ^mmu >mm10.kegg les mm10.kegg |perl -ne '$line=$_;$id=(split)[0];$gene=(split/:/,$id)[1];if($line=~/(K\d{4})/g){print "$gene\t$1\n"}' >mm10.ko

• Genome索引
  染色體大小
  wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes

轉載于:https://www.cnblogs.com/raisok/p/10917749.html

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