I receive the following error when I try to create a txdb from a gff file that I imported into GRanges:
> GenomicFeatures::makeTxDbFromGRanges(test) Error in .get_cds_IDX(type, phase) : the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
However, when I check the GRanges object, everything seems to be in order:
> cds <- which(test$type == 'CDS') > table(test[cds]$phase) 0 12519 > which(test[cds]$phase != 0) integer(0)
Can someone point in me the right direction what I am missing here? Thanks!