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

Dao