Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Re-assembly of singletons?

    Hi, all

    I have 454 transcriptome data, and I am a bit puzzled by some assemblies I have been doing. When I did a first assembly (on CLC Workbench), the ~600,000 reads assembled into 13,000 contigs and 157,000 singletons. Just out of curiosity, I used the set of singletons and did a new assembly of them. Since they were supposedly unmatched reads, I expected them to not assemble very well, if at all. Instead, the singletons assembled into a new set of 14,000 contigs, leaving a remaining 70,000 singletons!! I used the same stringency for both assemblies (0.5 length fraction, and 0.90 identity).

    When I look at the coverage for the re-assembled singletons, it seems they have comparable coverage and length distribution to the original assembly. So they seem to be OK.

    I guess I don't really understand the assembly algorithm, cause I am a bit puzzled as to why it would leave so many reads unassembled in a first pass, when they were obviously matched to other reads.

    So my question is: is re-assembly of 'left-over' singletons from a first assembly a reasonable approach? Or does that somehow force 'bad' contigs to be formed?

    Any insight would be extremely helpful, since the structure of my dataset will vary tremendously depending on the answer!

    Thanks!

    Felipe

  • #2
    the same concern...

    Comment


    • #3
      Keep in mind that CLC GWB is not a transcriptome but a genome assembler. That might lead to unforseen results. You may want to ask CLC support tocomment on the results you have gotten.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM
      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 05-24-2024, 07:15 AM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 10:28 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 07:35 AM
      0 responses
      20 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-22-2024, 02:06 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Working...
      X