Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cufflinks merging nearby genes

    Hi everyone,

    I'm running Cufflinks (v 0.9.3) on one of my datasets (human, 50 bp PE, around ~600-700 million reads), and tried to assemble transcripts without prior annotation.

    For the most part, the program works very well. However, when genes adjacent to one another (intergenic distance on the order of a small/medium-sized intron) are the same strand, Cufflinks merge multiple genes into one transcript. I've attached a picture of this example, where DVL2 & PHF23 are both part of the same Cufftranscript.

    Would anyone have any recommendations to fix this or reduce the chances of it happening? Since the intergenic distance is short, tweaking the "max-intron-length" flag in Cufflinks probably won't help here.

    Thanks!
    Attached Files

  • #2
    This problem is most likely being caused by polymerase run off on the 3' end of the PHF23 gene.

    It is possible, in principle, to identify two distinct genes from such data if the coverage is substantially different. However at this time the Cufflinks assembler does not explicitly take such information into account (it does in phasing alternative transcripts).

    A new forthcoming feature in Cufflinks to be released in the next version is a "reference guided assembly" where you can inform the assembler based on existing annotation. In this case, the resulting assembly would contain the two known genes thus preventing your problem. The nice thing is that the reference guided assembler will still allow for the discovery of new transcripts. Coming soon.

    Comment


    • #3
      Thanks! It definitely looks like polymerase run-off, so it'll be great to use the new Cufflinks feature for using reference assemblies to separate these merged genes.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        The Impact of AI in Genomic Medicine
        by seqadmin



        Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
        02-26-2024, 02:07 PM
      • seqadmin
        Multiomics Techniques Advancing Disease Research
        by seqadmin


        New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

        A major leap in the field has
        ...
        02-08-2024, 06:33 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:12 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-23-2024, 04:11 PM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-21-2024, 08:52 AM
      0 responses
      73 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-20-2024, 08:57 AM
      0 responses
      62 views
      0 likes
      Last Post seqadmin  
      Working...
      X