建立hg19版本的gtf

1:下载knownGene.txt.gz:
ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz

2:下载genePredToGtf:http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf

3:gzip -d refGene.txt.gz

4:cut -f 2- refGene.txt > refGene.input

5:genePredToGtf file refGene.input hg19refGene.gtf

6:cat hg19refGene.gtf | sort -k1,1 -k4,4n > hg19refGene.gtf.sorted

参考链接：http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format