Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to do target mapping efficiently

    Dear All,

    I would like to align the reads to some target genome region (for example, the gene I am interested in in the reference genome). Is there any efficient way to do this kind of target mapping instead of align the reads to the whole genome? For example, maybe I can extract the target gene sequences I am interested in in the reference genome, and make a new file? Is that possible?


    Thanks!

    Best,

    Sadiexiaoyu

  • #2
    You could extract the target gene sequence and map to it, but it's more accurate to map to the whole genome to avoid mismapping of ambiguous reads.

    Comment


    • #3
      You can make a new reference containing only the target sequence, and align to that, and that would be faster.

      But as Brian said, if you have reads that don't align there, you run the risk of forcing them to align to your target when they map better elsewhere.

      Comment


      • #4
        Originally posted by Brian Bushnell View Post
        You could extract the target gene sequence and map to it, but it's more accurate to map to the whole genome to avoid mismapping of ambiguous reads.
        Ahha, yes, you are right!

        Comment


        • #5
          Originally posted by swbarnes2 View Post
          You can make a new reference containing only the target sequence, and align to that, and that would be faster.

          But as Brian said, if you have reads that don't align there, you run the risk of forcing them to align to your target when they map better elsewhere.
          Yes, I agree with you. Thanks for the reply!

          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, 02-28-2024, 06:12 AM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          70 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          77 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X