Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    Find SNP in Sanger sequenced gene

    Hi guys,
    I have about 120 sequences of the same genes from our sample, which are sequenced by Sanger methods, How can I get the SNP sites among this gene compared to the reference gene? Is there any software can help me do this?

    Any sugestion will be highly appreciated!
    Tags: None
  • #2
    My recommendation would be to align the reads to your reference using the long read option in BWA or Lastz (or something else with long read capacity) and output a SAM file. You should be able to get SNPs out of the SAM file pretty easily following the SAM Tools FAQ here
    SAM tools
    http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ
    Download SAM tools for free. SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format.


    Will that do the trick?

    Comment

    • #3
      hello everyone
      I am a new member

      Comment

      Previous template Next

      Latest Articles

      Collapse
      • seqadmin
        Non-Coding RNA Research and Technologies
        by seqadmin




        Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

        Nobel Prize for MicroRNA Discovery
        This week,...
        10-07-2024, 08:07 AM
      • seqadmin
        Recent Developments in Metagenomics
        by seqadmin





        Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
        09-23-2024, 06:35 AM
      View All

      ad_right_rmr

      Collapse

      News

      Collapse
      Topics Statistics Last Post
      Mechanical Forces in DNA Transcription Uncovered by Clemson Researchers by seqadmin
      Started by seqadmin, 10-02-2024, 04:51 AM
      0 responses
      103 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      10-02-2024, 04:51 AM  
      New Epigenetic Clock Links Cheek Cells to Mortality Risk by seqadmin
      Started by seqadmin, 10-01-2024, 07:10 AM
      0 responses
      111 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      10-01-2024, 07:10 AM  
      AI-Powered Blood Test Shows Promise for Early Ovarian Cancer Detection by seqadmin
      Started by seqadmin, 09-30-2024, 08:33 AM
      1 response
      114 views
      0 likes
      		 Last Post EmiTom
      by EmiTom
      10-07-2024, 06:46 AM  
      Stem Cell Research Suggests Human Cells May Enter Developmental Pause by seqadmin
      Started by seqadmin, 09-26-2024, 12:57 PM
      0 responses
      20 views
      0 likes
      		 Last Post seqadmin
      by seqadmin
      09-26-2024, 12:57 PM  
      View All
      Working...
      X