How to get starting and ending positions of 5'UTRs and 3'UTRs?

[Loczi94]

Hi everyone!

I have a gff file with genome annotations downloaded from NCBI (http://www.ncbi.nlm.nih.gov/genome/23338). Does anyone know if there is any easy way to get starting and ending positions of 5'UTRs and 3'UTRs for that genome?

I hope that someone would be able to answer me, cause I need this informations to go on with my project. Thanks in advance

[dpryan]

If you download the GFF file from that link you'll notice that the UTRs aren't explicitly labeled, which is too bad. You might be able to use R to create a TxDB object from that GFF file:

library("GenomicFeatures")
gff = makeTxDbFromGFF("GCF_000633615.1_Guppy_female_1.0_MT_genomic.gff")
fiveUTRsByTranscript(gff)

There's also a threeUTRsByTranscript() function.

[Loczi94]

Warning messages

Thank you very much. I've done that, but I got some warning messages:

1: In '.extract_exons_from_GRanges(exon_IDX, gr, ID, Name, Parent, feature = "exon", ':
The following orphan exon were dropped (showing only the 6 first):
seqid start end strand ID Parent Name
1 NC_024338.1 11587093 11587135 - id225630 id225629 id225630
2 NC_024338.1 11586584 11586996 - id225631 id225629 id225631
3 NC_024338.1 11599024 11599069 - id225633 id225632 id225633
4 NC_024338.1 11598612 11598925 - id225634 id225632 id225634
5 NC_024338.1 11601674 11601728 - id225636 id225635 id225636
6 NC_024338.1 11601296 11601594 - id225637 id225635 id225637
2: In 'makeTxDbFromGRanges(gr, metadata = metadata)':
The following transcripts were dropped because their exon ranks could
not be inferred (either because the exons are not on the same
chromosome/strand or because they are not separated by introns):
gene23263

I found some tips here: https://support.bioconductor.org/p/69716/ , but I'm not sure if it's appropriate for my problem.

[dpryan]

Those are sort of weird regions, they have CDS but no annotated exons. If you look through the file, they're annotated as undergoing VDJ recombination (meaning that they're presumably immune related). I'm not sure how things get annotated like this and why they then lack exons, but that's the cause of the error. You can essentially ignore these warnings, since the only way to fix them would be to add a bunch of fake exons to the files and I can't say with certainty that that'd be correct.