Refseq annotation | Populus trichocarpa
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
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Hs stands for homo sapiens, so you cannot work with any plants here. See whether NCBI provides gene annotations for this species.
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.
Thanks, I have the GTF file from NCBI
It's just that i simply don't know how to use it in R
You can load it with the import function of rtracklayer.