I am in the process of doing enrichment analysis for DEG in Atlantic salmon. To do so, I need to convert the gene names that came out of STAR/HTseq to the same format, so they are uniform.

Results sample:

# A tibble: 1,053 × 1
   id          
   <chr>       
 1 LOC106612275
 2 LOC106611534
 3 LOC100380739
 4 LOC106610718
 5 LOC106573648
 6 btk         
 7 LOC106613810
 8 LOC106571198
 9 LOC106582786
10 gria4       
# … with 1,043 more rows

I used biomaRt,

ensembl <- useEnsembl(biomart = 'genes', dataset = 'ssalar_gene_ensembl')
gene_id <- getBM(attributes = c('entrezgene_accession', 'entrezgene_id'),
                            filters = 'entrezgene_accession',
                            values = sig_res,
                            uniqueRows = T,
                            mart = ensembl)

And got the conversions,

> head(gene_id)
  entrezgene_accession entrezgene_id
1                abce1     100194739
2                 abi1     100195035
3               acadvl     106602820
4               afg3l2     106597060
5                aggf1     106568194
6                  agt     100195417

However, when I joined the converted IDs with the initial gene list supplied to biomaRt, I noticed that there was a mismatch of 191 genes that did not convert.

> nrow(sig_res) - nrow(gene_id)
[1] 191

By looking at the concatenated list of initial + converted, there are indeed a few genes that did not get their gene IDs assigned.

> sig_res %>% left_join(gene_id, by = c('id' = 'entrezgene_accession')) %>% 
+   mutate(complete_id = if_else(is.na(entrezgene_id), id, entrezgene_id)) %>%
+   mutate(complete_id = gsub('LOC', '', complete_id)) -> full_sig_res

> arrange(full_sig_res, desc(complete_id))
# A tibble: 1,060 × 3
   id      entrezgene_id complete_id
   <chr>   <chr>         <chr>      
 1 wdfy4   NA            wdfy4      
 2 vcan    NA            vcan       
 3 timm9   NA            timm9      
 4 rps6kc1 NA            rps6kc1    
 5 ptpn14  NA            ptpn14     
 6 ppp1r17 NA            ppp1r17    
 7 nckp1   NA            nckp1      
 8 mk67i   NA            mk67i      
 9 klf7    NA            klf7       
10 ki67    NA            ki67       
# … with 1,050 more rows

For example, by looking at one of the genes that did not get converted, wdfy4, it shows up on NCBI in Atlantic salmon, with a gene ID, but it does not show up on Ensembl. On Ensembl, it only returns results for human.

Now I reckon this is related with the fact that I used RefSeq's Atlantic salmon annotation for the initial alignment and gene count, while Ensembl's version is used by biomaRt for the ID conversion. Does anyone have an idea how I can solve this issue? i.e. convert all the unconverted gene names to gene IDs.