Question: same transcript with different values in cuffdiff
0
gravatar for Ly, Dao
4.0 years ago by
Ly, Dao20
Canada
Ly, Dao20 wrote:

Hi

I'm have been searching on the forum but couldn't find answer for my specific question.  I'm analyzing the cuffdiff of transcripts differential expression result and found that for some of the transcripts same accession number they have different values.  I understand that gene has different isoforms but if the accession number is the same hence same isoform why would cuffdiff returns 2 different values.  I'm including 2 examples of my cuffdiff output any explanation is greatly appreciated.

Thanks

example 1:                                                                                                                                                                                                                                                                                                                             

gene_id                gene           gene name locus                                 status                                          value_1 value_2 log2(fold_change) test_stat p_value q_value significant

                                                                                                                                                                    

XLOC_000155 NM_014675 CROCC chr1:17066807-17299474     OK 9.0882 3.96956 -1.19502 -2.3658 0.00085 0.007793 yes
XLOC_000155 NM_014675 CROCC chr1:17066807-17299474     OK 0.899119 0.56106 -0.68036 -0.47306 0.5079 0.700695 no
XLOC_000155 NM_014675 CROCC chr1:17066807-17299474     NOTEST 0.082748 0.13062 0.658588 0 1 1 no

example 2:

XLOC_000097 NM_001014765 FBXO44 chr1:11708417-11723384     OK 0.489105 0.789976 0.691666 0.084265 0.8371 0.913847 no
XLOC_000097 NM_183412 FBXO44 chr1:11708417-11723384     OK 1.08216 1.08248 0.000421 6.81E-05 0.97535 0.9858 no
XLOC_000097 NM_001014765 FBXO44 chr1:11708417-11723384     OK 1.65389 2.20919 0.41766 0.089671 0.90105 0.947527 no
XLOC_000097 NM_001014765 FBXO44 chr1:11708417-11723384     OK 2.1139 1.49908 -0.49583 -0.10367 0.88185 0.93797 no
XLOC_000097 NM_033182 FBXO44 chr1:11708417-11723384     OK 13.2691 19.5032 0.555641 0.317543 0.56475 0.74297 no
XLOC_000097 NM_183413 FBXO44 chr1:11708417-11723384     OK 28.9029 31.8086 0.1382 0.111997 0.84295 0.917138 no
XLOC_000098 NM_018438 FBXO6 chr1:11724149-11734409     OK 6.27812 7.10025 0.177536 0.327834 0.619 0.780796 no

 

 

 

 

rna-seq cuffdiff • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by Ly, Dao20

I have the same problem. I use the Ensembl gtf file. I don't understand why this is happening.

ADD REPLYlink written 20 months ago by onemoreuser0
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Check the reference GTF dataset that you are using. Are the gene_id and transcript_id attributes assigned to the same value (transcript_id)? This can result from certain sources. Try using the one from iGenomes. A copy for hg19 is located on the public Main Galaxy server ready to use in 'Shared Data -> Data Libraries -> iGenomes'.

Thanks, Jen, Galaxy team

 

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k

I'm having a similar problem and I downloaded the iGenomes files like you suggested, but the files that are supposed to be from NCBI don't look like NCBI to me. In the fasta files the chromosome is named '1', '2' and so on... these are not the NCBI chromosome names. I download the NCBI build37.2 for Mus Musculus.

ADD REPLYlink modified 20 months ago • written 20 months ago by onemoreuser0
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