Cufflinks version higher than 1.3.0 gives 0 DEG

Question

[debashis.bioinfo]

Hi,

I am using Cufflinks 2.2.2(new release) package for differential gene expression analysis between control and treated sample. It gives 0 DEG. Also I try all Cufflinks version higher than 1.3.0 (2012) which gives same result. But when I am using Cufflinks 1.3.0, It gives 3880 DEG.

Please suggest me to solve this issue.

Thanking you,
Debashis

[TriS]

could you post the command lines you used? have you checked the differences between the versions?

[debashis.bioinfo]

Hello sir, Here I have attached the command and result of both version

cufflinks 2.2.1

cufflinks  -p 4 -o cufflinks_control -G gene.gtf aln_sorted.sam

RES:

Chromosome    Cufflinks    transcript    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; FPKM "198.7189985737"; frac "1.000000"; conf_lo "153.587491"; conf_hi "243.850506"; cov "550.743971";
____________________________________________________________________________________^^^^^^_____________________________^^^^^^^^^^^^^^^^^^^^^^
Chromosome    Cufflinks    exon    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; exon_number "1"; FPKM "198.7189985737"; frac "1.000000"; conf_lo "153.587491"; conf_hi "243.850506"; cov "550.743971";
______________________________________________________________________________^^^^^^______________________________________________^^^^^^^^^^^^^^^^^^^^^

cufflinks -p 4 -o cufflinks_treated -G gene.gtf aln_sorted.sam

Chromosome    Cufflinks    transcript    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; FPKM "30.9499112892"; frac "1.000000"; conf_lo "17.978468"; conf_hi "43.921355"; cov "115.363614";
____________________________________________________________________________________^^^^^^_____________________________^^^^^^^^^^^^^^^^^^^^
Chromosome    Cufflinks    exon    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; exon_number "1"; FPKM "30.9499112892"; frac "1.000000"; conf_lo "17.978468"; conf_hi "43.921355"; cov "115.363614";
______________________________________________________________________________^^^^^^______________________________________________^^^^^^^^^^^^^^^^^^^^

cuffdiff 2.2.1

cuffdiff -p 4 -o diff  cuffcmp.combined.gtf control/aln_sorted.sam treated/aln_sorted.sam

RES:

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    BG04_4    Chromosome:2416-2680    q1    q2    OK    113.98    50.4509    -1.17583    -1.64999    0.10395    0.896442    no
______________________________^^^^^^______________________________________________^^^^^^____^^^^^^^___________________________________________________^^

cufflinks 1.3.0

/usr/local/src/cufflinks-1.3.0.Linux_x86_64/cufflinks --no-update-check -p 4 -o cufflinks_control -G gene.gtf aln_sorted.sam

RES:

Chromosome    Cufflinks    transcript    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; FPKM "198.6925307440"; frac "1.000000"; conf_lo "153.983218"; conf_hi "243.401843"; cov "550.743971";
____________________________________________________________________________________^^^^^^_____________________________^^^^^^^^^^^^^^^^^^^^
Chromosome    Cufflinks    exon    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; exon_number "1"; FPKM "198.6925307440"; frac "1.000000"; conf_lo "153.983218"; conf_hi "243.401843"; cov "550.743971";
______________________________________________________________________________^^^^^^______________________________________________^^^^^^^^^^^^^^^^^^^^

/usr/local/src/cufflinks-1.3.0.Linux_x86_64/cufflinks --no-update-check -p 4 -o cufflinks_treated -G gene.gtf aln_sorted.sam

RES:

Chromosome    Cufflinks    transcript    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; FPKM "30.9469137217"; frac "1.000000"; conf_lo "18.041159"; conf_hi "43.852669"; cov "115.363614";
____________________________________________________________________________________^^^^^^_____________________________^^^^^^^^^^^^^^^^^^^^
Chromosome    Cufflinks    exon    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; exon_number "1"; FPKM "30.9469137217"; frac "1.000000"; conf_lo "18.041159"; conf_hi "43.852669"; cov "115.363614";
______________________________________________________________________________^^^^^^______________________________________________^^^^^^^^^^^^^^^^^^^

cuffdiff 1.3.0

/usr/local/src/cufflinks-1.3.0.Linux_x86_64/cuffdiff -p 4 cuffcmp.combined.gtf control/aln_sorted.sam treated/aln_sorted.sam

RES:

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    BG04_4    Chromosome:2416-2680    q1    q2    OK    227.688    33.6473    -2.7585    5.62029    1.90637e-08    3.1755e-07    yes
______________________________^^^^^^______________________________________________^^^^^^^____^^^^^^^_______________________________________________________^^^

Thanking You,
Debashis