Columns in CuffDiff_gene_exp.diff
test_id - Ensembl gene ID
gene_id - Ensembl gene ID
gene - Gene name
locus - chromosome and location of the gene
sample_1 - sample label (q1) (Day 0)
sample_2 - sample label (q2) (Last Day)
status - Can be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing.
value_1 - FPKM of the gene in sample q1
value_2 - FPKM of the gene in sample q2
log2(fold_change) - The (base 2) log of the fold change q1/q2
test_stat - The value of the test statistic used to compute significance of the observed change in FPKM
p_value - The uncorrected p-value of the test statistic
q_value - The FDR-adjusted p-value of the test statistic
significant - Can be either "yes" or "no", depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing

Columns in Cufflinks_(day0|LastDay)_rep[1-2]_genes.fpkm_tracking
tracking_id - Ensembl gene ID
class_code - The class_code attribute for the object, or "-" if not a transcript (should be - if a gene)
nearest_ref_id - The reference transcript to which the class code refers
gene_id - The gene_id(s) associated with the object
gene_short_name - The gene_short_name(s) associated with the object
tss_id - The tss_id associated with the object, or "-" if not a transcript/primary transcript, or if tss_id isn't present
locus - chromosome and location of the gene
length - The number of base pairs in the transcript, or '-' if not a transcript/primary transcript
coverage - Estimate for the absolute depth of read coverage across the object
FPKM - FPKM of the object in sample
FPKM_conf_lo - the lower bound of the 95% confidence interval on the FPKM of the object in sample 
FPKM_conf_hi - the upper bound of the 95% confidence interval on the FPKM of the object in sample 
FPKM_status - Quantification status for the object in sample 0. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution.