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  • Introduction

    Hello All:

    I am new to RNA-seq and am using an Ion Proton instrument to generate data. Learning to process the data has been very frustrating because I don't know how to run command-line scripts. I've been working with some commercial software, but they are very expensive and don't do all the things I would like.

    I would love to have a contact who works with Proton data and would be willing to answer some basic questions for me.

    Thanks, Alison

  • #2
    Are you actually running (working on) a Proton sequencer or just using the data from a one?

    Comment


    • #3
      Both! I have a technician who assists with running the instrument. We are also having issues with the RNAse III digestion on the bench side.

      Comment


      • #4
        Is torrent suite not helping with basic analysis (since there is a GUI)? What kind of data analysis are you doing?

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        • #5
          If you upgrade to torrent suite 4.6, there is a new RNA-Seq plugin with new plots, tables and downloadable tables.

          Comment


          • #6
            I'm currently using Partek, which is great for doing the 2 step alignment but I have to purchase an additional piece of software to get RPKM values from the bam files.

            I will upgrade the torrent suite and see if the plug-in is helpful.

            Thank you GenoMax and genehunter!

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