Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 11:49 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-24-2024, 08:47 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Working...
X