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Agilent Fragment Analyzer - Does it really need an SC?

  • 1.  Agilent Fragment Analyzer - Does it really need an SC?

    Posted 9 days ago
    Edited by Andor Kiss 6 days ago

    Considering buying an Agilent FA 5200 to QC nucleic acids, need to be able to size large PacBio libraries.  Do I really need an SC or is this instrument pretty stable and worry free?



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    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------



  • 2.  RE: Agilent Fragment Analyzer - Does it really need an SC?
    Best Answer

    Posted 8 days ago
    We have had both the Fragment Analyzer and the Femto.  Both are finicky little beasts.  It has absolutely been beneficial for us to have the SC on both, as we have had to have an entire instrument replaced and bad arrays, etc.  I also will say that the Femto, when it behaves, is much more accurate at sizing the PacBio libraries.  We were overshearing our samples because the FA was overestimating the sizes dramatically.  That being said, the femto comes with it's own headaches and to keep it semi-professional, is temperamental.  I still think the switch to Femto (about 1.5 years ago) was worth it, but I will always keep my eye open for a non-Agilent competitor!  Good luck!!

    Elizabeth Hudson

    Assistant Director

    University of Louisville Sequencing Technology Center

    Dept. Biochemistry & Molecular Genetics

    319 Abraham Flexner Way

    HSC-A, Room 601

    Louisville, KY 40202

     

    eahunt02@louisville.edu

    (502) 852-4996




    Original Message


  • 3.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago
    Seconding Elizabeth - we have also found our FA to be the most finicky of our instruments and the one that we've needed service on the most.  We also see the oversizing that she mentions for large libraries - if that's specifically what you intend to use the system for, a Femto is a more accurate option.

    Marie



    Original Message


  • 4.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago
    Edited by Andor Kiss 6 days ago

    Yes, we just got a PacBio VEGA, and the main need is sizing of large libraries and greater sensitivity.  Glad to have asked about the FA - it seems for us, the Femto might be a lot better choice.  We're on a BA2100 still and so either will be a major leap!



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


  • 5.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago

    Okay thanks - glad I asked.



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


  • 6.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago
    Our NGS group has switched to Tape Station, but we still use the FA for our Nucleic Acid QC services in my group.


    Original Message


  • 7.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago

    Just to clarify; are you saying that you use the TapeStation to size & QC large (~20 kbp) fragments?



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


  • 8.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 7 days ago
    We use our FA primarily for that (we do ONT, not PacBio), though we aren’t completely happy with how well it works. Our NGS lab says the Tape Station is about the same for that purpose. We are looking at a new pulse field box from Sage Biosciences (Pippin Pulse II) as a possibly cheaper and more accurate option, but that system isn’t out yet, so I can’t tell you how well it works.


    Original Message


  • 9.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 6 days ago

    Interesting, I did not know about the PPII.  Yeah, the Femto is extremely expensive, so I thought that the FA might be a better compromise, but I'm starting to re-think that.



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


  • 10.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago
    In our experience, that instrument absolutely requires a service contract. It breaks down frequently.

    Roxann


    Original Message


  • 11.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 8 days ago

    Thanks!



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


  • 12.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 7 days ago

    Our lab's FA has always been very robust. We have a service contract, but have not needed it for repairs - we replace the capillary ourselves but get an annual PM where the instrument is cleaned and the fluidics tubing is replaced. Issues we've had have been related to samples or reagents.

    We do restrict its use to trained operators (it's not a shared instrument) and adhere to cleaning and maintenance schedules. We also found that the 96-capillary array did not work for us - it was too easy for samples over the assay concentration range to bleed signal into surrounding capillaries. The 48-cap array works fine for our throughput.

    One caveat: our instrument is older and was manufactured by the original company that was later purchased by Agilent (Advanced Analytical). I don't know if there have been changes to the design/manufacture since then.



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    Daniella Wilmot
    Research Associate IV
    UMass Chan PacBio Core
    Shrewsbury MA
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    Original Message


  • 13.  RE: Agilent Fragment Analyzer - Does it really need an SC?

    Posted 6 days ago

    We are a training core, so once a user is trained, they are free to use (most) instrumentation at will.  Although, as you can imagine different users have differing skill sets. Thanks for the tip on the 96 cap array - we wouldn't be using that - too much throughput for us, but good to know.



    ------------------------------
    Andor Kiss - Center for Bioinformatics & Functional Genomics
    Director
    Miami University
    Oxford OH
    ------------------------------

    Original Message


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