Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Jolin
    Member
    • Oct 2011
    • 10

    #1

    Why can't cuffdiff identify splicing difference

    I made simulation RNA-Seq data of one gene by FLUX. This gene has two isoforms. The ratio of the isoforms in the first sample is 0:100, while in the second sample 100:0. I ran the cufflinks, cuffcompare and cuffdiff, but the "splicing.diff" produced by cuffdiff showed that no significant splicing were found. But according to the "isoform_exp.diff", the FPKM of these two isoforms vary a lot in two samples. Why is the "test_stat" so small and why can't cuffdiff identify the splicing difference of this gene?

    The content of splicing.diff is as follows:
    test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
    TSS1 XLOC_000001 A1_2_6 chr:4900-11900 test1 test2 OK 0 0 0.746756 2.07E-73 1 1 no

    The content of isoform_exp.diff is as follows:
    test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant
    TCONS_00000001 XLOC_000001 A1_2_6 chr:4900-11900 test1 test2 OK 261123 633.471 -6.02153 5.62055 1.90E-08 3.81E-08 yes
    TCONS_00000002 XLOC_000001 A1_2_6 chr:4900-11900 test1 test2 OK 19398.3 300439 2.74006 -4.17333 3.00E-05 3.00E-05 yes

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 10:52 AM
0 responses
10 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
19 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-13-2026, 09:56 AM
0 responses
17 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-09-2026, 11:14 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Working...