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  • Any idea on primer trimming tool?

    I was looking at some sequence data generated by Sanger Sequencer ABI 3730 xl. Is there any recommended tool to do the primer trimming?

    And if it is possible, is there any tool to sequencing trimming, since I want to discard the QC<20.. Thanks

  • #2
    We use 'phred' to do quality trimming from the .abi file. If you already have the sequence & quality then any program that handles both (e.g., in fastq format) should work.

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    • #3
      Originally posted by westerman View Post
      We use 'phred' to do quality trimming from the .abi file. If you already have the sequence & quality then any program that handles both (e.g., in fastq format) should work.
      Thanks for your info!

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      • #4
        We have used phred for basecalling and lucy[1] for quality and primer trimming for years. We used cross_match for contamination screening. Lucy 2 has a GUI and is designed for interactive work[2].

        [1] = http://lucy.sourceforge.net/
        [2 ]= http://www.complex.iastate.edu/downl...cy2/index.html
        Last edited by sklages; 09-23-2013, 10:52 AM. Reason: :-)

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        • #5
          Originally posted by sklages View Post
          We have used phred for basecalling and lucy[1] for quality and primer trimming for years. We used cross_match for contamination screening. Lucy 2 has a GUI and is designed for interactive work[2].

          [1] = http://lucy.sourceforge.net/
          [2 ]= http://www.complex.iastate.edu/downl...cy2/index.html
          Thanks sklages!

          Actually I tried both cmd and gui version. It seems it does not have the option to trim primer. Could u provide one example? Thanks again!

          =====================================

          And I also tried the Geneious Software, it can do the trimming as well.
          Last edited by arkilis; 09-23-2013, 05:53 PM.

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          • #6
            Hmm, "primer trimming" = "vector removal at 5' and 3' end"?
            If so, have a look at '-vector'. It takes a vector file in fasta format and a splice site file describing the site where the insert has been cloned into the plasmid or the flanking PCR primers from PCR reaction, depending what kind of sample you have.
            Have a look at the man page, where the options, including the format of the splice site file, are described extensively. If you have cDNA sequences it is even capable of trimming polyA/T at the end of reads.
            For sanger data it is probably the "tool to go" if you are a on linux and a bit familiar with scripting perl/bash/whatever. It is flexible and very fast.
            I don't know if the lucy2 GUI version has the same options as cmd line lucy has. You'll have to check this.

            Geneious is nice, GUI-only, not that flexible and not for free.

            So as always, it depends on what you wanna do and how much effort you want to put into this .. ;-)

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