Error when making TxDb object from gtf file
Entering edit mode
3 months ago
bowden • 0


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?

Thank you

gtf Xenopus RStudio TxDb • 247 views

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