I have been trying to analyze a rat Solid SRA but I encountered a problem:  
cufflinks gave me 0 RPKM in all genes.   Here is my workflow

1.        Get data with EBI SRA: sent the fastaq file directly to galaxy

2.       Fastaq groomer

3.       Mapped with bowtie for Solid (paire-ended) with the built- in index 
rat rn5 as reference genome

4.       Sam to Bam the bowtie mapping result

5.       Cufflinks the bam file

All RPKMs of gene expression and transcript expression have a 0 value even 
thought the RPKM status is OK.  I used default setting for all jobs.  Am I 
missing something?  Any help, suggestion will be greatly appreciated.  Thank 
you very much
Best regards
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