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  • cufflinks problem with coverage and FPKM values

    Hi !
    It's the first time I use the Cufflinks tool and I need help.
    I used the -g option (RABT assembly) to search novel genes and isoforms in a yeast annotated genome. The RNA-Seq data are Illumina 50 bp single-end oriented reads. I run Cufflinks with default parameters :
    cufflinks -g file.gff reads.fastq.sorted.bam
    The output seems correct, but I have a lot of genes with coverage=0, FPKM=0, FPKM_conf_lo=0 and FPKM_conf_hi not equal to 0 but with a very low value. I think that these genes are expressed, probably weakly expressed.
    My question is: what parameters/options should I change in the cufflinks command to obtain non-zero values of coverage and FPKM ?
    Thanks a lot for your answers.
    Laurence

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