Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cufflinks counts vs. rsem counts

    Hi all!
    i have reference transcriptome with 76,000 contigs that ware built with trinity(DeNovo) from my experiment.
    Next, i wanted to know counts per contig.
    I started with rsem and i got table of 76,000 contigs with count per contig.
    When trying to get count table with cufflinks i got table of 42,000 contigs.
    How can it be?
    Cufflinks dosent refer to some contigs in purpose?
    Any ideas?

    Thanks

  • #2
    This post is very old, but I am going to reply for others to benefit from my answer,

    The result you got for cufflinks makes sense, since, cufflinks perform abundance estimation by two steps, the first step is a transcript assembly then the second step will be quantitation or abundance estimation, so i think, cufflinks assembled some of these contigs into larger contigs, this is why the number of contigs outputted from cufflinks is lesser than from rsem,

    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
    11 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