Hi, I have a problem with adding REFSEQ IDs to the SummarizedExperiment object, containing ENSEMBL transcripts and quantification information from Salmon. I have a tximeta_1.0.3 version. I used makeLinkedTxome:

indexPath <-"/usr/users/asawick/ania/U2OS4sU060319/salmon/Homosapiens.GRCh38.cdna.allindex" fastaPath <-"/usr/users/asawick/ania/U2OS4sU060319/salmon/Homosapiens.GRCh38.cdna.all.fa" gtfPath <- "/usr/users/asawick/ania/U2OS4sU060319/salmon/Homosapiens.GRCh38.96.gtf"

makeLinkedTxome(indexDir=indexPath, source="Ensembl", organism="Homo Sapiens", release="38", genome="GRCh", fasta=fastaPath, gtf=gtfPath, write=FALSE)

The object (st in this case) looks ok:

rowRanges(st)
GRanges object with 168526 ranges and 6 metadata columns:
seqnames ranges strand | tx_id
|
ENST00000434970 14 22439007-22439015 + | ENST00000434970
ENST00000448914 14 22449113-22449125 + | ENST00000448914
ENST00000415118 14 22438547-22438554 + | ENST00000415118
ENST00000604446 15 21010494-21010516 - | ENST00000604446
ENST00000603693 15 21011451-21011469 - | ENST00000603693
... ... ... ... . ...
ENST00000635145 20 29878636-29879363 - | ENST00000635145
ENST00000617915 1 159972548-159974064 - | ENST00000617915
ENST00000455649 X 133989443-133990086 + | ENST00000455649
ENST00000278882 20 30377372-30399257 + | ENST00000278882
ENST00000644453 9 131370933-131372514 + | ENST00000644453
tx_biotype tx_cds_seq_start tx_cds_seq_end

ENST00000434970 TR_D_gene 22439007 22439015
ENST00000448914 TR_D_gene 22449113 22449125
ENST00000415118 TR_D_gene 22438547 22438554
ENST00000604446 IG_D_gene 21010494 21010516
ENST00000603693 IG_D_gene 21011451 21011469
... ... ... ...
ENST00000635145 unprocessed_pseudogene
ENST00000617915 unprocessed_pseudogene
ENST00000455649 unprocessed_pseudogene
ENST00000278882 unprocessed_pseudogene
ENST00000644453 unprocessed_pseudogene
gene_id tx_name

ENST00000434970 ENSG00000237235 ENST00000434970
ENST00000448914 ENSG00000228985 ENST00000448914
ENST00000415118 ENSG00000223997 ENST00000415118
ENST00000604446 ENSG00000270824 ENST00000604446
ENST00000603693 ENSG00000270451 ENST00000603693
... ... ...
ENST00000635145 ENSG00000283020 ENST00000635145
ENST00000617915 ENSG00000273933 ENST00000617915
ENST00000455649 ENSG00000232068 ENST00000455649
ENST00000278882 ENSG00000149531 ENST00000278882
ENST00000644453 ENSG00000285287 ENST00000644453

seqinfo: 47 sequences from GRCh38 genome

But I get the following error: library("org.Hs.eg.db")

st <-addIds(st, column = "REFSEQ", gene = F)
Error in addIds(st, column = "REFSEQ", gene = F) :
requireNamespaceorgpkg.name, quietly = TRUE) is not TRUE

package "org.Hs.eg.db" is installed.

Do you maybe know what I'm overlooking?

Thank you, Anna

We look up the correct organism in tximeta using the string that you specify, where Homo Sapiens gives HS as the string. This would work if you specify the organism in makeLinkedTxome as Homo sapiens.