How to get --transcript-to-gene-map <file> in RSEM?

Question

[John]

Hi dear one,

In reference building step in RSEM, there is an option "--transcript-to-gene-map <file>", for transcriptome references, say mouse's mm9 transcriptome from ensemble release 67, what would be the file to be used as --transcript-to-gene-map <file> and where I can find it? what is that file really means?

thanks in advance!

Answer 1

[h.mon]

The --transcript-to-gene-map is explained at the rsem-prepare-reference help page, or just issuing rsem-prepare-reference at the command-line. In addition to the suggestions from the help, you can also use biomaRt or the org.Mm.eg.db R packages to build this file, something along the lines:

mart_11 <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "organism_gene_ensembl", host = 'mar2015.archive.ensembl.org')

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = mart_11)

t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)

See posts here, here and here.