Hi, I am using the Kallisto-Sleuth pipeline for differential expression of RNA-seq and I am having a problem with performing 'sleuth_prep' in Sleuth. It's my first time to use R package Sleuth, I dont know how solve the problem, any help would be fantastic for me!
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) library(sleuth) so <- sleuth_prep(s2c, ~ condition, target_mapping = t2g, extra_bootstrap_summary = TRUE) reading in kallisto results dropping unused factor levels ..... normalizing est_counts 26768 targets passed the filter normalizing tpm merging in metadata Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file. Warning message: In check_target_mapping(tmp_names, target_mapping, !is.null(aggregation_column)) : 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.