tophat / cufflinks annotation data

[jwhite]

Hello,

Both tophat and cufflinks accept annotation files as arguments (in the form of GTF files). I am processing 30 samples from mouse RNA-seq data, but find NO annotation in my output files. I have checked the following:

1) that the BAM files and GTF files use the same chromosome nomenclature, ie chrN
2) that the reference genome files use the same nomenclature, ie chrN
3) that the GTF file is usable by tophat, ie gtf_juncs <gtf_name> yields appropriate results.

I expected to see gene symbols or refseq IDs in the output, but found neither. Below is and example of one of the transcripts.gtf output files, and the first few lines of the GTF file. Shouldn't the annotation be added to the transcripts.gtf file if the GTF option is provided? Or am I missing something here?

Is there a tool in the tophat or cufflinks packages that will add the annotation? Or will I have to write that myself?

Thanks for any help you can supply.
Cheers,
Joe


transcripts.gtf

chr1 Cufflinks transcript 4481088 4483630 1000 - . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "0.1707050811"; frac "1.000000"; conf_lo "0.098790"; conf_hi "0.240801"; cov "2.589206";
chr1 Cufflinks exon 4481088 4482749 1000 - . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "0.1707050811"; frac "1.000000"; conf_lo "0.098790"; conf_hi "0.240801"; cov "2.589206";
chr1 Cufflinks exon 4483181 4483630 1000 - . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "0.1707050811"; frac "1.000000"; conf_lo "0.098790"; conf_hi "0.240801"; cov "2.589206";
chr1 Cufflinks transcript 4766459 4775776 1000 - . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "1.0690828163"; frac "0.790339"; conf_lo "0.749463"; conf_hi "1.370969"; cov "15.665388";
chr1 Cufflinks exon 4766459 4766882 1000 - . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "1.0690828163"; frac "0.790339"; conf_lo "0.749463"; conf_hi "1.370969"; cov "15.665388";
chr1 Cufflinks exon 4767606 4767729 1000 - . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "2"; FPKM "1.0690828163"; frac "0.790339"; conf_lo "0.749463"; conf_hi "1.370969"; cov "15.665388";
[...]

mm9/genes.gtf

chr1 unknown exon 3204563 3207049 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown stop_codon 3206103 3206105 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown CDS 3206106 3207049 . - 2 gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown CDS 3411783 3411982 . - 1 gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown exon 3411783 3411982 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown CDS 3660633 3661429 . - 0 gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown exon 3660633 3661579 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown start_codon 3661427 3661429 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id "NM_001011874"; tss_id "TSS1978";
chr1 unknown exon 4280927 4283093 . - . gene_id "Rp1"; gene_name "Rp1"; p_id "P11404"; transcript_id "NM_001195662"; tss_id "TSS19117";
chr1 unknown stop_codon 4283062 4283064 . - . gene_id "Rp1"; gene_name "Rp1"; p_id "P11404"; transcript_id "NM_001195662"; tss_id "TSS19117";
[...]