Question: Looking for 3'-UTR and 5'-UTR sequences
1
gravatar for Marcos Lancia
18 months ago by
Argentina
Marcos Lancia10 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 • 594 views
ADD COMMENTlink modified 18 months ago by Devon Ryan1.9k • written 18 months ago by Marcos Lancia10
1
gravatar for Devon Ryan
18 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k 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 COMMENTlink written 18 months ago by Devon Ryan1.9k
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