cuffcompare -CG CDS entry lost

[Edden]

Hi,

a problem with GFF files.

I using an "unusal" Gff file:

http://www.candidagenome.org/download/gff/C_glabrata_CBS138/archive/C_glabrata_CBS138_version_s02-m01-r03_features.gff

In order to use cufflinks with this annotation, I used

cuffcompare -s genome_seqs.fa -CG -r annotation.gtf annotation.gtf

This produced a GFF which contains both, tss_id's and p_id's, but no cds entries. Strangely, this new GFF only has exon entries and no CDS entries (even though the original has both)
In the next steps (cufflinks, cuffmerge, cuffcompare,) I don't have any p_id's which finally results in empty cds test when using cuffdiff.

Any idea why I loose CDs entries?

[Edden]

Any suggestions?

[jb2]

I'm also interested in a potential answer to this. I've merged a few gtf annotation files together using cuffcompare. These all have p_ids, and also lose the CDS data from the original gtf files. However, when using these union gtf files with cuffmerge, the p_ids are then lost because there is no CDS entries in the union gtf file. Anyone know if there is anyway to keep the p_id entries when doing the above?