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.goecks@emory.edu> Para: Cristian Rojas <cristianrojasbr@yahoo.com.ar> CC: galaxy-user@lists.bx.psu.edu Enviado: miércoles, 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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