topgo - biomart query

[jorgeboucas]

    host=stringr::str_split("${params.biomart_host}", "/biomart")[[1]][[1]]
    ensembl = useMart("ensembl",dataset="${params.biomart_dataset}", host=host)
    goterms = getBM(attributes = c("ensembl_gene_id", 
                                            "external_gene_name",
                                            "go_id", "name_1006"),  
                              filters = 'ensembl_gene_id',
                              values = Din[, 'ensembl_gene_id'],
                              mart = ensembl)

for topgo this code block should be run first as an individual process and the output saved to a txt file. Only then the different topgo for the respective comparisons should take place based on the txt file.

[jorgeboucas]

table is already available under /workdir/deseq2_output/annotated/biotypes_go_raw.txt