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Question: Looking for 3'-UTR and 5'-UTR sequences
1
gravatar for Marcos Lancia
22 months ago by
Marcos Lancia • 10
Argentina
Marcos Lancia • 10 wrote:

Hi everyone! I have a question, I hope you can help me out. I have a list of genes that I´d like to obtain their 5'-UTR and 3'-UTR sequences. I work with Medicago truncatula, and I have RNA-SEQ data to work with. Any idea?? Thanks so much.
3'-utr 5'-utr • 756 views
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modified 22 months ago by Devon Ryan • 1.9k • written 22 months ago by Marcos Lancia • 10
1
gravatar for Devon Ryan
22 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

This is easiest to do in R (within Galaxy, I presume you could use one of the interactive environments) with the GenomicFeatures and rtracklayer bioconductor packages:

library(GenomicFeatures)
library(rtracklayer)
txdb = makeTxDbFromGFF("Mt4.0v1_genes_20130731_1800.gff3")
utr5p = fiveUTRsByTranscript(txdb, use.names=T)
utr3p = threeUTRsByTranscript(txdb, use.names=T)
export.bed(utr5p, "5pUTR.bed")
export.bed(utr3p, "3pUTR.bed")

The 5pUTR.bed and 3pUTR.bed files are BED12 files, though you could export GFF3 or GTF files if you preferred. I'll take the liberty of uploading the 3' and 5' BED12 files so you can also just download them.
ADD COMMENT • link written 22 months ago by Devon Ryan • 1.9k
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