missing mm39.rna.gtf.gz annotation file in https://github.com/bcbio/bcbioR/tree/main/inst/extdata/annotation

[ggrimes]

I am running the template https://github.com/bcbio/rnaseq-reports/blob/main/01_quality_assessment/quality_assessment.qmd

and inside it call the load_data.R script.

The https://github.com/bcbio/rnaseq-reports/blob/main/00_libs/load_data.R on line 84 creates a link to

https://github.com/bcbio/bcbioR/raw/refs/heads/main/inst/extdata/annotation/mm39.rna.gtf.gz which doesn't exist

if the genome is set to mm39

 if (genome == "other") {
    gtf <- gtf_fn
  } else {
    if (genome == "hg38") {
      gtf <- "hg38.rna.gtf.gz"
    } else if (genome == "mm10") {
      gtf <- "mm10.rna.gtf.gz"
    } else if (genome == "mm39") {
      gtf <- "mm39.rna.gtf.gz"
    }
    gtf <- file.path("https://github.com/bcbio/bcbioR/raw/refs/heads/main/inst/extdata/annotation", gtf)
  }

If you set the genome to other and set the gtf file to the gtf you used, it works ok.

[lpantano]

this is true, we need to add that chink of gtf to bcbioR, thanks for pointing this out.

[lpantano]

I think it should work not