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ag1805x/tx2gene_fasta

Created September 18, 2019 07:44
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Code to generate tx2gene from reference transcriptome for use with tximport() in R
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tx2gene_fasta
# Code to generate tx2gene from reference transcriptome for use with tximport() in R
# Reference transcriptome: wget ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
zcat Homo_sapiens.GRCh38.cdna.all.fa.gz | grep '>' | cut -d ' ' -f1,4,7 > temp
paste <(cut -d '>' -f2 temp | cut -d ' ' -f1) <(cut -d ' ' -f2 temp | cut -d ':' -f2) <(cut -d ' ' -f3 temp | cut -d ':' -f2) >> tx2gene.txt
rm temp
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ag1805x commented Jun 22, 2021

It would be great if you could post the output files here itself..

I think the file was too big to be uploaded to Git. That is why I have put the link to download the reference genome as well. This way you could do it for any version of the Ensembl genome.

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