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