Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SFF file - primers

    Hello!
    I am using 454 Roche Junior, I have few questions about reads of sff file.
    I have splitted a SFF file into individual SFF file (according to their MIDs), I don't understand if I have to do also remove primers in the reads or if they are already removed.
    Please could you explain me the structure of a read in general?
    Thank you in advance

  • #2
    Primers should already be removed, both the primers that are used for sequencing and the MID sequences. When in doubt, you could use prinseq, it will try to detect adaptor sequences. http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi.

    Comment


    • #3
      Thank you very much for your response. I have another question: is it a problem if my amplicon is longer than final read and it is possibile that the end (3') of my read is incomplete?

      Thank you in advance for your attention!

      Comment


      • #4
        A problem for what? Depends on your further analysis steps, I guess?

        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
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X