annotateCircs() returns a variety of gene_id values for circs with both flanks intergenic

BIMSBbioinfo / ciRcus

An R package for annotation of circular RNAs

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annotateCircs() returns a variety of gene_id values for circs with both flanks intergenic #16

Closed retaj closed 7 years ago

retaj commented 7 years ago

o_O

> table(circs.diff.dt[feature=="intergenic:intergenic"]$gene_id)

                 0 ENSMUSG00000062352         intergenic     no_single_host 
                28                  1                303               1851

mschilli87 commented 7 years ago

Is that a new 'feature' or was it always like that and we just missed it in previous versions? Did try to install from master or even older (poor man's git bisect)?

retaj commented 7 years ago

It is also broken in master. Not sure if it ever worked properly, but given that we have ~0 users, I will not waste time investigating :)

retaj commented 7 years ago

There are still situations where an intergenic circRNA gets a gene ID, but these are either caused by external annotation (see Ensembl 75 for chr12:109447067-109451813) or legit (two non-overlapping transcirpts of the same gene). These could be handled differently but are very rare + current solution is not wrong so I'll close this...