Hi everyone, I am a bit confused about a painful step of my pipeline using Sleuth. I am trying to move from the transcript level to the gene level and that's why I am using biomaRt (?).
devtools::install_github('pachterlab/sleuth', ref = 'devel', force=TRUE) mart <- biomaRt::useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", host = 'ensembl.org') mart 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) so <- sleuth_prep(s2c, target_mapping = t2g)
at this point the output is the following one:
so <- sleuth_prep(s2c, target_mapping = t2g) reading in kallisto results dropping unused factor levels ...... normalizing est_counts 47250 targets passed the filter normalizing tpm merging in metadata summarizing bootstraps ...... Warning messages: 1: In check_num_cores(num_cores) : It appears that you are running Sleuth from within Rstudio. Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1. If you wish to take advantage of multiple cores, please consider running sleuth from the command line. 2: In check_target_mapping(tmp_names, target_mapping) : intersection between target_id from kallisto runs and the target_mapping is empty. attempted to fix problem by removing .N from target_id, then merging back into target_mapping. please check obj$target_mapping to ensure this new mapping is correct.
I can't understand the problem because I am pretty sure I have already created a table with the specific gene names and they match!
target_id ens_gene ext_gene 333 ENSMUST00000148678 ENSMUSG00000020225 Tmbim4
PS: please pardon my ignorance in term of bioinformatic jargon