Created
March 10, 2015 23:08
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Convert RefFlat genes to exon list
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| curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz" \ | |
| | gunzip -c \ | |
| | awk '{n=int($9); split($10,S,/,/);split($11,E,/,/); for(i=1;i<=n;++i) {printf("%s\t%s\t%s\t%s\n",$3,S[i],E[i],$1);} }' \ | |
| > refFlat.exons.hg19.bed | |
| bedtools sort -i refFlat.exons.hg19.bed > refFlat.exons.hg19.sorted.bed |
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