Question: problems about cuffdiff output
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gravatar for 512788522
4.4 years ago by
51278852220
China
51278852220 wrote:

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  mutNOTEST  0       0       0       0       1       1       no
XLOC_000004     XLOC_000004     OR4F3   chr1:367658-368597      normal  mut     NOTEST  0       0 00       1       1       no

 


 

 

 


 

rna-seq • 1.5k views
ADD COMMENTlink written 4.4 years ago by 51278852220
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