add gene names from RefSeq instead of ENSEMBL using biomaRT for sleuth when reading kallisto output

Question

[Abiterkuile]

Hi there,

I have reads that have been aligned using Kallisto constructed with a Refseq reference transcriptome (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_rna.fna.gz). In order to include gene names into transcript-level analysis in Sleuth (an R package), I need to add the gene names using a Reqseq human trancriptome however in the Sleuth walk-through there are only instructions on how to do this using ENSEMBL (for an example data set constructed with the ENSEMBL human transcriptome);

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl",
  host = 'ensembl.org')
t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
    "external_gene_name"), mart = mart)
t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id,
  ens_gene = ensembl_gene_id, ext_gene = external_gene_name)

from: https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html

Does anyone know how i can do this but with RefSeq?

Thanks

Answer 1

[Emily]

RefSeq don't really have gene names but you can get the NM transcript IDs with:

t2g <- biomaRt::getBM(attributes = c("refseq_mrna", "external_gene_name"), mart = mart)