Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Align reads to 1 gene

    Hi All,

    I need to align ABI Solid reads to just 1 gene to see how many reads align to just that gene. (No mapping has been done so far). I need to know what is the best way to do this. It seems like an over kill for me to create a reference file, index etc for 1 gene and then align the read files using any aligner (I am leaning towards NovoalignCS but other suggestions with reasons are welcome). Is there a simpler method to do this kind of single gene alignment for reads?

    Thanks,

    Vishal

  • #2
    Geneious works very well for this. You just select the gene sequence and the list of reads and use the map to reference function.

    Comment


    • #3
      Depending on how you did your experiment, be cautious in mapping to a single gene.

      If you sequenced an entire genome/transcriptome and map this only to a single gene, then reads that should map to other locations may end up being incorrectly being mapped to that gene, inflating the number of reads mapping to it.

      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
      49 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