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  • pingu
    Member
    • Jul 2015
    • 26

    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
  • flxlex
    Moderator
    • Nov 2008
    • 412

    #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

    • pingu
      Member
      • Jul 2015
      • 26

      #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

      • flxlex
        Moderator
        • Nov 2008
        • 412

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

        Comment

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