Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Issues with cuffdiff

    Hello,

    I'm performing an analysis containing 3 samples per conditions and 5 conditions (so 15 samples in total). I want to do pairwise comparison for each condition.

    I'm just starting using cuffdiff.
    Firsly I just tested cuffdiff with only 2 conditions, like that :

    Code:
    cuffdiff -L control,A -p 16 --library-type fr-firststrand --no-update-check  reference.gtf control_1.bam,control_2.bam,control_3.bam A_1.bam,A_2.bam,A_3.bam

    And I obtained 3 differentially expressed genes in the gene_exp.diff file.

    Then I tried to do all my comparisons in one command line :

    Code:
    cuffdiff --output-dir allComparisons  -L control,A,B,C,D -p 16 --library-type fr-firststrand --no-update-check  reference.gtf control_1.bam,control_2.bam,control_3.bam A_1.bam,A_2.bam,A_3.bam B_1.bam,B_2.bam,B_3.bam C_1.bam,C_2.bam,C_3.bam D_1.bam,D_2.bam,D_3.bam

    And looking at the gene_exp.diff file in output, I obtained 2 differentially expressed genes between control and A which only one in common with the 3 genes I obtained before.

    Which analysis I should trust ?
    And what is the good way to use cuffdiff ?
    Last edited by ClemBuntu; 11-18-2015, 01:05 AM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X