Hi Simon, 

I have not changed the count files (except their file names) or the flattened GFF after running dexseq_count.py. For example:
---
lsa-579-005:DEXSeq_tra2b_Named darwin$ grep 'bmp2\b' CTR1.txt 
bmp2:001	160
bmp2:002	45
bmp2:003	47
lsa-579-005:DEXSeq_tra2b_Named darwin$ grep 'bmp2\b' flat_frog_q1_fixed_v2.gff 
scaffold_5	merged_stranded_q1.GFF	aggregate_gene	101514148	101526061	.	-	.	gene_id "bmp2"
scaffold_5	merged_stranded_q1.GFF	exonic_part	101514148	101516034	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "001"; gene_id "bmp2"
scaffold_5	merged_stranded_q1.GFF	exonic_part	101522614	101522972	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "002"; gene_id "bmp2"
scaffold_5	merged_stranded_q1.GFF	exonic_part	101525481	101526061	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "003"; gene_id "bmp2"
---
What I tried to say in what you quote is that using the same data set (same aligned reads) and an very similar flat GFF I can run DEXSeq without problems. In that case I took the combined.GTF from Cufflinks and flattened it. However, in that case the gene_name from the Cufflinks GTF is lost and gene_id is the not very readable "XLOC" ID that Cufflinks use to keep track of genes: 
---
dichmann@genepool01:/global/projectb/scratch/dichmann/HTSeq_frog_q1$ grep 'XLOC_021009' flat_frog_q1.gff merged.gtf 
flat_frog_q1.gff:scaffold_5	merged_stranded_q1.GFF	aggregate_gene	101514148	101526061	.	-	.	gene_id "XLOC_021009"
flat_frog_q1.gff:scaffold_5	merged_stranded_q1.GFF	exonic_part	101514148	101516034	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "001"; gene_id "XLOC_021009"
flat_frog_q1.gff:scaffold_5	merged_stranded_q1.GFF	exonic_part	101522614	101522972	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "002"; gene_id "XLOC_021009"
flat_frog_q1.gff:scaffold_5	merged_stranded_q1.GFF	exonic_part	101525481	101526061	.	-	.	transcripts "TCONS_00042267"; exonic_part_number "003"; gene_id "XLOC_021009"
merged.gtf:scaffold_5	Cufflinks	exon	101514148	101516034	.	-	.	gene_id "XLOC_021009"; transcript_id "TCONS_00042267"; exon_number "1"; gene_name "bmp2"; oId "PAC:20701023"; nearest_ref "PAC:20701023"; class_code "="; tss_id "TSS27823"; p_id "P24249";
merged.gtf:scaffold_5	Cufflinks	exon	101522614	101522972	.	-	.	gene_id "XLOC_021009"; transcript_id "TCONS_00042267"; exon_number "2"; gene_name "bmp2"; oId "PAC:20701023"; nearest_ref "PAC:20701023"; class_code "="; tss_id "TSS27823"; p_id "P24249";
merged.gtf:scaffold_5	Cufflinks	exon	101525481	101526061	.	-	.	gene_id "XLOC_021009"; transcript_id "TCONS_00042267"; exon_number "3"; gene_name "bmp2"; oId "PAC:20701023"; nearest_ref "PAC:20701023"; class_code "="; tss_id "TSS27823"; p_id "P24249";
---

So I changed the flattened GFF so that it has the human-sensible gene_name instead of the gene_id, where possible and run dexseq_count.py using that flat GFF.

Hope it makes sense. Btw, I used HTSeq-0.5.4p3.

I guess I could hack it and add the gene names to the final DEXSeq output, but since I see myself using this package a lot, I would to figure out what is going on.

Cheers, 
Darwin

On May 24, 2013, at 1:05 PM, Simon Anders <anders@embl.de> wrote:

> Hi Darwin
> 
>> FWIW, DEXSeq works on the same data set, but with a slightly
>> different flat GFF (the one that gives me trouble have been changed
>> the gene names). The GFF is flattened from a Cufflinks GTF.
> 
> Wait, what do you mean by "changed the gene names"?
> 
> Each count file has two columns, one with the gene IDs, the other with the counts. The flattened GFF file also contains the gene ID, and to make sure that count files and GFF file fit together, DEXSeq compares the gene IDs and complains if they don't match.
> 
>  Simon
> 
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