Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Removing primers

    Hey all,

    I am new to using gsAssembler. I want to do an assembly of cDNA sequences. However, they have primers attached to it. I saw an option called 'Trimming database for De-Novo assembly, and provided the list of primers as an input. However, when I check the output assembly, several contigs still have those primers. How do I make sure that these are removed before assembly( I have a .sff file).
    Also, I want all the contigs after assembly. The AllContig.fna in gsAssembly is not listing all the contigs ( like the singletons). How do I obtain all the contigs from the assembly?

    Thanks in advance for the help,

    Regards,

  • #2
    The -v option is probably what you describe, and if it does not remove all primers I guess there is a bug in gsAssembler :-(

    Singletons are not contigs (by definition, I guess), but I do understand you want to get them included in your final dataset.

    Using the sffinfo trick described in the software manual on page 134 (getting the read IDs from the 454ReadStatus.txt file, make a new sff file with only the singletons, and then extracting the reads as a fasta file) would do it.

    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
    9 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