Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cuffdiff output

    Hi everyone,

    I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
    CuffSet instance with:
    2 samples
    0 genes
    0 isoforms
    0 TSS
    0 CDS
    0 promoters
    0 splicing
    0 relCDS
    What might be the problem here? I would really appreciate any help in this regard.
    Thanks in advance!

  • #2
    did you get solution? I got same and psoted here :
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    may expect your view ?
    Thank you


    Originally posted by kasutubh View Post
    Hi everyone,

    I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
    CuffSet instance with:
    2 samples
    0 genes
    0 isoforms
    0 TSS
    0 CDS
    0 promoters
    0 splicing
    0 relCDS
    What might be the problem here? I would really appreciate any help in this regard.
    Thanks in advance!

    Comment

    Latest Articles

    Collapse

    • 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
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Working...
    X