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.
On Mar 30, 2011, at 11:31 AM, Cristian Rojas wrote:
> Thanks Jeremy. I did it.
> ----- Mensaje original ----
> De: Jeremy Goecks <jeremy.goe...@emory.edu>
> Para: Cristian Rojas <cristianroja...@yahoo.com.ar>
> CC: email@example.com
> Enviado: miércoles, 30 de marzo, 2011 12:02:47
> Asunto: Re: [galaxy-user] Trouble with RNAseq analysis
> Please share your history with me (History Options --> Share/Publish -->
> with User --> my email) and I'll take a look.
> 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
>> 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
>> same. Any advice? What was wrong?
>> Thanks in advance.
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: