why cuffdiff cds-tests empty?

[joseph]

Hi

I ran cuffcompare with the reference annotation "refGene.gtf" which is RefSeq Genes (refGene) track from UCSC GB.

cuffcompare -V -r refGene.gtf -R -o s7_s8_refGene transcripts_s7.gtf transcripts_s8.gtf

I noticed that in the "*.combined.gtf" output there is an attribute oId instead of p_id:

chr1	Cufflinks	exon	4797909	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "1"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1";
chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "2"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1";

When I ran cuffdiff, the "cds.diff" and "cds.fpkm_tracking" files came out empty:

cuffdiff -N -L s_7,s_8 -p 2 -v -r ~/mm9.fa s7_s8_refGene.combined.gtf accepted_hits_s7.bam accepted_hits_s8.bam

..........
Processed 18302 loci. Performed 4816 isoform-level transcription difference tests
Performed 574 tss-level transcription difference tests
Performed 2853 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 203 splicing tests
Performed 131 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking

Any suggestions will be appreciated.
Thanks

[honey]

Cds

Assuming you are working with hg19- Use hg19.fa file and -s option while running cuffcompare

[joseph]

cds

Assuming you are working with hg19- Use hg19.fa file and -s option while running cuffcompare

That solved the problem. Thank you for caring and answering my question.
Joseph