Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • control and test in DE in RNA-seq

    I have been analyzing the mRNA-seq data using Cuffdiff and has two questions:

    1. In case of Differential expression analyis between a control vs test sample, ln fold change is represented as Value2/ Value1 as per the manual of Cufflink. I was wondering Value 1 should be control while Value 2 should be test sample.
    From Cufflink manual:
    FPKMx 8.01089 FPKM of the gene in sample x
    FPKMy 8.551545 FPKM of the gene in sample y
    ln(FPKMy/FPKMx) 0.06531 The natural log of the fold change y/x

    2. In typical control vs test sample based on Hg19 reference annotation- I get around 36K transcripts (total including no test and test OK) that seems to be little less as expected. Does it seem to be right number?

    3. When I combine/ filter combined GTF file with any of isoform.exp file I get
    RIC8A chr11:202907-236320 OK chr11 207163 208938 exon 1
    RIC8A chr11:202907-236320 OK chr11 209271 209318 exon 2
    RIC8A chr11:202907-236320 OK chr11 209407 210000 exon 5

    Here the combined GTF provide a location (in red) Chr11 202907-236320 while cufdiff provide exon spanning 207163 208938. What is the first location refer to It is referring to neither gene location nor longest transcript. Any suggestion please.
    Thanks
    Last edited by honey; 04-18-2011, 09:56 PM.

  • #2
    Question

    Any suggestion please.

    Comment

    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, 03-27-2024, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X