Hi 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
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