I am trying to generate a TxDb object from a Xenopus laevis gtf file in RStudio. These are my dependencies
BiocManager::install(c("GenomicFeatures", "BiocGenerics", "S4Vectors", "IRanges", "GenomeInfoDb","GenomicRanges", "AnnotationDbi"))
And this is my code
txdb <- GenomicFeatures::makeTxDbFromGFF("XENLA_9.2_Xenbase.Chromosomes.scaffolds.gtf")
The message I get is below
Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... some transcripts have no "transcript_id" attribute ==> their name ("tx_name" column in the TxDb object) was set to NAthe transcript names ("tx_name" column in the TxDb object) imported from the
"transcript_id" attribute are not uniqueError in .make_splicings(exons, cds, stop_codons) : some CDS cannot be mapped to an exon
Does anyone know what is causing this error and how I could attempt to resolve it?