converting a hg19 refGene.txt to

作者: 苏牧传媒 | 来源:发表于2018-08-25 21:53 被阅读10次

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

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