Hi,
a problem with GFF files.
I using an "unusal" Gff file:
http://www.candidagenome.org/downloa...3_features.gff
In order to use cufflinks with this annotation, I used
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?
a problem with GFF files.
I using an "unusal" Gff file:
http://www.candidagenome.org/downloa...3_features.gff
In order to use cufflinks with this annotation, I used
Code:
cuffcompare -s genome_seqs.fa -CG -r annotation.gtf annotation.gtf
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?
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