Bioinformatics one-liner * Day 19
1/ create a tx2gene mapping file from ensemble gtf retaining the version number of genes and transcripts. A thread. #bioinformatics #oneliner #unix
1/ create a tx2gene mapping file from ensemble gtf retaining the version number of genes and transcripts. A thread. #bioinformatics #oneliner #unix
2/ awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f2,4| sed 's/\"//g' | awk '{print $1"."$2}' > genes.txt
3/
awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f6,8| sed 's/\"//g' | awk '{print $1"."$2}' > transcripts.txt
paste transcripts.txt genes.txt > tx2genes.txt
awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f6,8| sed 's/\"//g' | awk '{print $1"."$2}' > transcripts.txt
paste transcripts.txt genes.txt > tx2genes.txt
That's a wrap!
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