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2 hours ago by

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.



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