Enter the body of text here I am new to R (R version 4.3.0) and RNAseq. As tutorial, I am using the paper 'RNA-Seq workflow: gene-level exploratory analysis and differential expression [version 2; peer review: 2 approved]" by Michael I Love et al and everything seems to well until now,

I have an error message stated below which worked well in the paper:

#Error in makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character()) : 
 could not find function "makeTxDbFromGFF"
Please how do I solve it?


> bamfiles <- BamFileList(filenames, yieldSize = 2000000)

> seqinfo(bamfiles[1])

Seqinfo object with 84 sequences from an unspecified genome:
  seqnames   seqlengths isCircular genome
  1           249250621       <NA>   <NA>
  10          135534747       <NA>   <NA>
  11          135006516       <NA>   <NA>
  12          133851895       <NA>   <NA>
  13          115169878       <NA>   <NA>
  ...               ...        ...    ...
  GL000210.1      27682       <NA>   <NA>
  GL000231.1      27386       <NA>   <NA>
  GL000229.1      19913       <NA>   <NA>
  GL000226.1      15008       <NA>   <NA>
  GL000207.1       4262       <NA>   <NA>

> gtffile <- file.path(dir,"Homo_sapiens.GRCh37.75_subset.gtf")


# > (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()))
# Error in makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character()) : 
could not find function "makeTxDbFromGFF"

You said it was not found after loading it but you didn't actually show that you loaded the library. Did you do a library("GenomicFeatures") call before this?

See @shepherl post above, but note that the up-to-date workflow uses tximport:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html