Question: I am trying to get tophat / cufflinks to work with Ensembl annotations.

Although this looks like a long post, my problem is quite simple: I keep getting CUFF.1, CUFF.2, CUFF.3, etc, as my geneid, in the genes.fpkmtracking file:

$ head genes.fpkm_tracking
tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status
CUFF.1 - - CUFF.1 - - chr1:568966-570302 - - 1080.24 1019.13 1141.36 OK
CUFF.4 - - CUFF.4 - - chr1:979748-982084 - - 19.74 10.1647 29.3153 OK
CUFF.2 - - CUFF.2 - - chr1:982297-984413 - - 11.6648 5.19434 18.1353 OK
CUFF.3 - - CUFF.3 - - chr1:881909-892399 - - 24.6448 15.3299 33.9596 OK

What I want is to have the Ensembl ENSG annotations, and possibly gene_name as well.

Yes, I realize the chromosome annotation (1st column) in the GTF/GFF file must match the FASTA header exactly.

I have tried the "native" Ensembl GTF file (chromosomes numbered 1, 2, 3..., X, Y, MT) and a bowtie2 genome index built from Ensembl's GRCh37.69 FASTA:

1 processed_transcript exon 11869 12227 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002234944";
1 processed_transcript exon 12613 12721 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002867822";
1 processed_transcript exon 13221 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002312635";

I have tried the native GTF with "chr" added in, and with the FASTA file modified in the same way (and of course bt2 index rebuilt):

chr1 processed_transcript exon 11869 12227 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002234944";
chr1 processed_transcript exon 12613 12721 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002867822";
chr1 processed_transcript exon 13221 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002312635";

I have also tried using cufflinks gffread utility, to make a GFF file from the above GTF file:

chr1 processed_transcript gene 11869 14412 . + . ID=ENSG00000223972;Name=DDX11L1;transcripts=ENST00000450305,ENST00000456328,ENST00000515242,ENST00000518655
chr1 processed_transcript misc_RNA 11869 14409 . + . ID=ENST00000456328;Parent=ENSG00000223972;geneID=ENSG00000223972;gene_name=DDX11L1;Name=DDX11L1-002;type=pseudogene
chr1 processed_transcript exon 11869 12227 . + . Parent=ENST00000456328
chr1 processed_transcript exon 12613 12721 . + . Parent=ENST00000456328
chr1 processed_transcript exon 13221 14409 . + . Parent=ENST00000456328

For which the corresponding bowtie2 index has these entries:

$ bowtie2-inspect -n /hulk/genomes/Ensembl/Homo_sapiens.GRCh37.69.dna.chromosome
chr10
chr11
chr12
chr13
...

I have even tried using the iGenomes files, with the same results!

The way I am running tophat and cufflinks is like this:

tophat -G Homo_sapiens.GRCh37.69.gtf --transcriptome-index=Homo_sapiens.GRCh37.69.genes -p 24 -o output Homo_sapiens.GRCh37.69.dna Sample1_1.fq.gz Sample1_2.fq.gz
cufflinks -p 6 -o output output/accepted_hits.bam

It is almost like I am running it without annotations, but the tophat / cufflinks programs never complain about being unable to match annotations with the FASTA file or anything:

[2012-11-09 17:11:40] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2012-11-09 17:11:40] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-11-09 17:11:40] Checking for Samtools
Samtools version: 0.1.18.0
[2012-11-09 17:11:41] Checking for Bowtie index files
[2012-11-09 17:11:41] Checking for reference FASTA file
[2012-11-09 17:11:41] Generating SAM header for /hulk/genomes/Ensembl/Homo_sapiens.GRCh37.69.dna.chromosome
format: fastq
quality scale: phred33 (default)
[2012-11-09 17:11:44] Reading known junctions from GTF file
[2012-11-09 17:12:02] Preparing reads
left reads: min. length=30, max. length=101, 999911 kept reads (89 discarded)
right reads: min. length=30, max. length=101, 999341 kept reads (659 discarded)
[2012-11-09 17:12:43] Creating transcriptome data files..
...snip...
[2012-11-09 18:10:58] Reporting output tracks
-----------------------------------------------
[2012-11-09 18:16:25] Run complete: 01:04:44 elapsed

You are using Cufflinks v2.0.2, which is the most recent release.
[18:16:26] Inspecting reads and determining fragment length distribution.
> Processed 120637 loci. [*************************] 100%
> Map Properties:
> Normalized Map Mass: 985482.42
> Raw Map Mass: 985482.42
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 163.12
> Estimated Std Dev: 50.10
[18:17:15] Assembling transcripts and estimating abundances.
> Processed 120951 loci. [*************************] 100%

Yes, this topic has been discussed online ad nauseum. Here, and here, and here, and many other places. I feel like I have read every possible internet page about this topic, but still the problem vexes me. In the past I once had this working just fine. In fact, I found that tophat / cufflinks worked very nicely with Ensembl annotations. However, it seems like something has changed -- either the software or the annotations? Am I the only one experiencing this? Can someone help me see what I am overlooking? Any help would be much appreciated.

Here are the software versions I am using:

$ bowtie2 --version
/usr/local/bin/bowtie2-2.0.2/bowtie2-align version 2.0.2
64-bit
Built on igm1
Wed Oct 31 23:16:47 EDT 2012
$ tophat --version
TopHat v2.0.6
$ cufflinks
cufflinks v2.0.2
linked against Boost version 104900

Answer: It doesn't appear that you're setting either the -G/--GTF or the -g/--GTF-guide flags when you run cufflinks. See comments above as well.