Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 1000 Genomes Data

    I am trying to count short tandem repeats (STR) from 1000 Genomes Project data using the low coverage BAM files, but am getting the same repeats even on known fast STRs. Should I be looking at other files within the project to do this? I am using SAMTools.

  • #2
    Depending on the aligner & parameters used, these may not have aligned well. In the worst case, no single read can contain the entire repeat array AND unique sequence on either side to enable conclusive mapping -- even if the repeat is not strictly too long, very long repeats will be unlikely to have randomly fragmented in such a manner that they can be uniquely mapped.

    STRs are definitely findable in the Watson & Venter BAM files & you might test out your method there. These were done with long read (454 & Sanger respectively) technologies that can read through all but the most ginormous repeats.

    My intern last summer developed a tool for this purpose; anyone interested in beta testing it can PM me about access. I'm trying to get some additional data generated to test it prior to releasing & publishing it -- the problem is a dearth of data in which the actual repeat length is known as tested by conventional methods. I know we looked at 1K genome data & thought she was able to pull variation out, but I'd need to check.

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