Hello everyone,

I am comparing two samples (control and treated) paired end RNA Seq data. I
am getting different FPKM values on my cufflinks output of 2 samples when
compared to the 2 values that cuffdiff..

Below is the snap shot of a gene with different FPKM values. (I am not
displaying the gene name).

Cufflinks output:

    Gene length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status Sample
xyz - - 39.9094 38.9553 40.8635 OK Control  xyz - - 19.4664 18.7786 20.1542
OK Treated

cuffdiff output:

     Gene  sample_1 sample_2 status value_1/Control value_2/ treated
log2(fold_change) test_stat p_value q_value significant  xyz q1 q2 OK
59.6706 27.1551 -1.1358 5.06151 4.16E-07 4.00E-05 yes

I am assuming that FPKM values from cufflinks and cuffdiff output should be
matching. Any kind of suggestions are appreciated.

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