Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MG-RAST KEGG mapper?

    Hi folks,

    I'm using MG-RAST to analyze my 454 metagenomic data and have run into an irritating feature - wondering if anyone has a workaround! In the KEGG map view, honing in on Nitrogen Metabolism, I can see the reads (blue) and contigs (red) mapped to different EC numbers, and when I hover over it will tell me how many sequences are mapped. The issue I'm having is that I ahve no way of accessing WHICH reads these are to analyze them further. Anyone have ideas?? I can't seem to find this same feature browsing or blasting the data, so I don't understand where the kegg mapper is getting this info....


    Thanks!!
    Attached Files

  • #2
    Try the following:

    -Click the analysis button upper right
    -Click on hierarchical classification
    -select your metagenome and annotation source KO (KEGG orthology)
    -ask for a table
    -hit generate
    -use filters or search for the function
    -when you find the function or enzyme the abundance number in blue is a link that opens a new tab with the reads corresponding to that function

    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, Yesterday, 06:37 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 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