problems about cuffdiff output

Question

[512788522]

After running TopHat, I hava run the following command directly(because of no replicates for each condition, i.e normal versus mutation):

cuffdiff -p 8 \
  -o ./cuffdiff_out \
  -L normal,mut \
  -u ./genes.gtf \
  ./tophat/accepted_hits.bam \
  ./tophat_mut/accepted_hits.bam

In addition, I also have performed the differential expression analysis in the following way:

cuffmerge -g ./genes.gtf \
  -p 8 \
  -o ./cuffmerge_out \
  -s ./ucsc.hg19.fa assembly.txt
cuffdiff -p 8 \
  -o ./diff_out \
  -L normal,mut \
  -u ./cuffmerge_out/merged.gtf \
  ./tophat/accepted_hits.bam \
  ./tophat_mut/accepted_hits.bam

There was great difference in their output. In the first way, the gene_exp.diff looked like:

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
A1BG    A1BG    A1BG    chr19:58858171-58874214 normal  mut     OK      33.5662 14.8501 -1.17654  -0.611634        0.50845 0.867476        no
A1BG-AS1        A1BG-AS1        A1BG-AS1        chr19:58858171-58874214 normal  mut     OK      1.17516    1.66153 0.499655        0.071299        0.84635 0.94951 no
A1CF    A1CF    A1CF    chr10:52559168-52645435 normal  mut     NOTEST  0       0       0       0 11       no

but in the second way, it looked like:

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_000001     XLOC_000001     DDX11L1 chr1:11873-29370        normal  mut     NOTEST  0       0 00       1       1       no
XLOC_000002     XLOC_000002     OR4F5   chr1:69090-70008        normal  mut     NOTEST  0       0 00       1       1       no
XLOC_000003     XLOC_000003     LOC100132062,LOC100133331       chr1:323891-328581      normal  mut      NOTEST  0       0       0       0       1       1       no