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.

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