一起生信啦啦啦RNASeq 数据分析

converting a hg19 refGene.txt to

2018-08-25  本文已影响10人  苏牧传媒

ref: Genes in gtf or gff format - genomewiki

1. Download your gene set of interest for hg19. For this example, I'll use the refGene table, but you can choose other gene sets, such as the knownGene table from the "UCSC Genes" track.

rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ./

2. Unzip

gzip -d refGene.txt.gz

3. Remove the first "bin" column:

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

4. Convert to gtf:

genePredToGtf file refGene.input hg19refGene.gtf

5. Sort output by chromosome and coordinate

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

上一篇 下一篇

猜你喜欢

热点阅读