Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • iGenomes data set....which to use?

    Can anyone shed any light on the relative merits of the 3 sources of reference data available on iGenomes (UCSC/NCBI/Ensembl)?

    Thanks

    Huw

  • #2
    They all (currently) share the same genome assembly for humans and mice.
    The differ in the annotation (where exactly are genes, what are they called, how do the transcripts look like?).

    I personally prefer to work with Ensembl, since they have a clear release policy (making it easy to reference the exact data you were using) , archives of older releases , a consistent set of 'stable ids' for genes/transcripts/proteins, the largest set of (chordata) genomes and provide backlinks for the evidence for each transcript.

    UCSC is often a bit more cutting edge, they have somewhat of an ongoing release process, nowadays include ENCODE genes (which in turn come from Ensembl...).

    Can't really say anything about the NCBI.

    So long,
    Florian

    Comment


    • #3
      Good question. I've heard anecdotally that using cufflinks with RABT assembly using refseq/ucsc gives you MANY more novel isoforms than when using Ensembl. Why or whether that's a bad thing, I'm not sure.

      Comment


      • #4
        @turnersed: Guess the first question is whether they're real 'novel' isoforms, or had already been in Ensembl.

        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
        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
        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