Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • why consed after Newbler

    Hi everyone,
    I'm just getting my feed wet with NGS thus my questions usualy appear to be very naive.

    My question this time is, why one should use another tool i.e. CONSED to deal with the result of an assembler i.e. Newbler even though the later
    does the trimming and removes the primers?

    thanx in advance.

  • #2
    For viewing the assembly, designing finishing primers, joining contigs together etc.

    It's not a required step if you want to just deal with the draft contigs.

    Quite helpful though. You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.

    Comment


    • #3
      Originally posted by nickloman View Post
      For viewing the assembly, designing finishing primers, joining contigs together etc.
      Necloman, thanks a lot for the replay. could you plese advise, why one should
      join the contigs to gether since we already get the consensus?

      Originally posted by nickloman View Post
      You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.
      really nice tool will check it

      Comment


      • #4
        Originally posted by nicedad View Post
        Necloman, thanks a lot for the replay. could you plese advise, why one should
        join the contigs to gether since we already get the consensus?
        Well, presumably your assembly is in fragments.

        In some circumstances you may want to join those together through some finishing experiments, perhaps there's a region of particular interest and it is split in two by a repeat.

        If you are lucky enough to have the assembly in a single contig then you don't need to do this, but it's pretty unusual!

        Comment


        • #5
          Do you mean that contigs must be joined to analyse a cDNA?
          if yeah, how to join them if the data are many Mbs?

          best,

          Comment


          • #6
            cDNAs are usually from mRNA (transcripts of protein expression) and thus are short, on the order of 1000 base contigs. A 454 project using Newbler with the '-cDNA' flag is excellent for creating complete contigs that can not and should not be further merged. We use Blast2Go to annotate our 454 runs.

            On the other hand, a whole genome shotgun assembly will almost always produce many contigs which can then be merged together into chromosomes (at least in theory) or at the very least into longer contigs. Using Consed or other tools will help scaffold and merge those contigs together or at least tell you what further work to do in order to get good merging.

            How to join them together? Usually requires more sequencing. Either directed or random. And much hoping that repeats don't get in the way. "Finishing" is a tough human-labor-requiring problem -- that is why there are so many unfinished genomes out there.

            Comment


            • #7
              nickloman, westerman, thanks for your patience!

              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
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              8 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