Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mauve-snps

    Hi- I am using Mauve to export SNPs (but I am not sure why I get more SNPs than it is published before)- for example snps between 2 bacterial strains should be 500 but I get > 2000 snps- any advice why does this happen, please?

  • #2
    Originally posted by mmmm View Post
    Hi- I am using Mauve to export SNPs (but I am not sure why I get more SNPs than it is published before)- for example snps between 2 bacterial strains should be 500 but I get > 2000 snps- any advice why does this happen, please?
    when you said "published before" do you refer to previous detected SNPs using mauve or another tool?
    SNP calling can vary between tools depending on how you mask low complexity regions.

    Comment


    • #3
      thank you very much for clarification- so do I mask low complexity regions using Mauve??

      Comment


      • #4
        Honestly I don't know, I'm not familiar with mauve algorithm.
        have you tried with Mummer 3? http://mummer.sourceforge.net
        I know Mummer can mask LCR.

        Comment


        • #5
          thanks- I am using Mauve at the moment, any one could explain getting many snps than actual snps using mauve? (any parametes should be adjusted)?

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • 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

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          25 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          28 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          24 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          52 views
          0 likes
          Last Post seqadmin  
          Working...
          X