Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Newbie dummy question, please help

    Hi, folks:
    I am doing research on Arabidopsis. The existing reference genome is on one ecotype (Col), and we have sequenced another ecotype (Ws), since we have mutants based on Ws.

    What should I do if I want to use Ws as a reference genome?
    I have used bowtie to align the Ws reads to Col and use Samtools/GATK try to find any indels/SNPs, however, my target is to be able to get a new reference genome based on Ws, what should I do?

    Any suggestions are much appreciated.
    Thx.

  • #2
    Newbie dunmmy question, please help

    Hi,


    You can do de-novo assembly using your Ws reads, with or without the Col genome as a reference genome.

    There are many programs for de novo assembly, depending on what type of sequencing data you have, Velvet, NIRA, Soapdenovo, and many others.

    best wishes,
    Maria

    Comment


    • #3
      Does it mean that I cannot use the already indexed reference genome at all?
      Thanks for your information

      Originally posted by mastal View Post
      Hi,


      You can do de-novo assembly using your Ws reads, with or without the Col genome as a reference genome.

      There are many programs for de novo assembly, depending on what type of sequencing data you have, Velvet, NIRA, Soapdenovo, and many others.

      best wishes,
      Maria

      Comment


      • #4
        If you use the reference genome then the assembly will be biased. You can assembly them de novo and then compare the assembled contigs to the reference genome instead

        Comment


        • #5
          If you don't mind me asking, what exactly are you trying to do. You say you have mutants in the Ws ecotype, so are you trying to use this sequencing data to map those mutations or did you sequence WT Ws to create a reference for this purpose? Or do you need the Ws genome for other purposes? I ask, because the optimal solution for what you are trying to do may be different than what you think.

          Ws is not so different from Col that it you cannot map to the Col reference.

          Furthermore, the Ws genome has already been assembled as part of the 1001 Genomes project.....so, the dirty work has already been done

          Comment


          • #6
            we have sequenced the mutants and ws. Thanks for your informaiton!!
            Would you educate me with what should I do if I know the mutant has a large chunk of insertion (up to 10kb possibly) and I wish to locate it, should I use reference genome based alignment or de novo, how?
            Thanks

            Originally posted by chadn737 View Post
            If you don't mind me asking, what exactly are you trying to do. You say you have mutants in the Ws ecotype, so are you trying to use this sequencing data to map those mutations or did you sequence WT Ws to create a reference for this purpose? Or do you need the Ws genome for other purposes? I ask, because the optimal solution for what you are trying to do may be different than what you think.

            Ws is not so different from Col that it you cannot map to the Col reference.

            Furthermore, the Ws genome has already been assembled as part of the 1001 Genomes project.....so, the dirty work has already been done

            http://mus.well.ox.ac.uk/19genomes/fasta/

            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
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            51 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