Refseq annotation | Populus trichocarpa

Question

[P]

Hello,

I would like to annotate a salmon output dataset with the RefSeq accession numbers (i.e NM_001404768.1, XM_002297615.4).

I keep coming across this way of doing it using org.Hs.eg.db, but it's not working with RefSeq and mostly plant organisms (as I work on Populus trichocarpa)

res$symbol <- mapIds(org.Hs.eg.db,
                     keys=rownames(res),
                     column="SYMBOL",
                     keytype="ENSEMBL",
                     multiVals="first")

Thank you

[ATpoint]

Hs stands for homo sapiens, so you cannot work with any plants here. See whether NCBI provides gene annotations for this species.

[GenoMax]

There are multiple genomes available for this plant. You can find the GTF files (and the transcriptome, one example) here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/775/GCF_000002775.5_P.trichocarpa_v4.1/

Depending on where you got the reference you could either use the GTF file or reanalyze using new transcriptome.

[P]

Thanks, I have the GTF file from NCBI

It's just that i simply don't know how to use it in R

[ATpoint]

You can load it with the import function of rtracklayer.