Question: Why Cuffdiff report more than one FPKM values for gene?
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20 months ago by
rice.researcher0 wrote:

I followed similar steps mentioned in the procedure part of Trapnell et al, 2012 for an RNASeq analysis of oryza sativa datasets. The problem I face is in the Cuffdiff output, where more that one FPKM value is reported for many genes as below,

  test_id   gene_id gene    locus   sample_1    sample_2    status  value_1 value_2 log2(fold_change)   test_stat   p_value q_value significant
 XLOC_005901    XLOC_005901 LOC_Os01g46440  Chr1:26422826-26425093  wild    mutant  OK  2.48243 8.09808 1.70582 0.193218    0.35875 0.999974    no
 XLOC_002129    XLOC_002129 LOC_Os01g46440  Chr1:26422826-26425093  wild    mutant  OK  26.4118 20.9721 -0.332716   -0.280221   0.63665 0.999974    no

 XLOC_003921    XLOC_003921 LOC_Os01g03040  Chr1:1159160-1164635    wild    mutant  OK  72.5969 77.3011 0.09058 0.0824954   0.8934  0.999974    no
XLOC_003922 XLOC_003922 LOC_Os01g03040  Chr1:1159160-1164635    wild    mutant  NOTEST  0.40255 0.306853    -0.391618   0   1   1   no

I have downloaded gff3 file and genome sequence info. from RGAP MSU database ftp. Tophat is of version 2.

Can anyone suggest me exactly what is going wrong here?


will be required to run again with annotation and genome index file from sources such as iGenomes?

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