Cristian,

The contig names in your GTF file don't match those in your reference (fasta) 
file. In order for Cufflinks to use a reference GTF, its contigs names must 
match those in your reference genome.

Best,
J.

On Mar 30, 2011, at 11:31 AM, Cristian Rojas wrote:

> Thanks Jeremy. I did it.
> Cristian
> 
> 
> 
> ----- Mensaje original ----
> De: Jeremy Goecks <jeremy.goe...@emory.edu>
> Para: Cristian Rojas <cristianroja...@yahoo.com.ar>
> CC: galaxy-user@lists.bx.psu.edu
> Enviado: miƩrcoles, 30 de marzo, 2011 12:02:47
> Asunto: Re: [galaxy-user] Trouble with RNAseq analysis
> 
> Cristian,
> 
> Please share your history with me (History Options --> Share/Publish --> 
> Share 
> with User --> my email) and I'll take a look.
> 
> Thanks,
> J.
> 
> On Mar 30, 2011, at 10:48 AM, Cristian Rojas wrote:
> 
>> Hi everybody, I am trying to analyze the differential expression between two 
>> RNAseq samples. But I found many troubles aligning my reads. I will describe 
>> what I did. First I groomed the FastQ files (2). Then I uploaded the Sorghum 
>> genome and aligned the reads to it with Tophat. Aftter that, I tried to use 
>> Cufflink with the BAM file of Tophat, using as annotation file an uploaded 
>> GTF 
> 
>> file and the Sorghum genome, but I received an error message in the three 
>> outputs of Cufflink. I tried to align against new brand Maize genome (now at 
>> Galaxy), and the same messages. I also converted the BAM file to SAM, but 
>> the 
>> same. Any advice? What was wrong?
>> Thanks in advance.
>> Cristian
>> 
>> 
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