Question: Looking for 3'-UTR and 5'-UTR sequences
gravatar for Marcos Lancia
22 months ago by
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 • 756 views
ADD COMMENTlink modified 22 months ago by Devon Ryan1.9k • written 22 months ago by Marcos Lancia10
gravatar for Devon Ryan
22 months ago by
Devon Ryan1.9k
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:

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 22 months ago by Devon Ryan1.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour