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Question: Error: the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
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gravatar for bbrink
5 weeks ago by
bbrink0
bbrink0 wrote:

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!

ADD COMMENTlink written 5 weeks ago by bbrink0

Would you mind providing a reproducible example and your `sessionInfo()`? Thanks!

ADD REPLYlink written 5 weeks ago by Hervé Pagès ♦♦ 13k

Also please tag your question properly i.e. with GenomicFeatures, not GenomicRanges. Thanks!

ADD REPLYlink written 5 weeks ago by Hervé Pagès ♦♦ 13k
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