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Old 07-08-2015, 07:19 AM   #1
avnairn
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Location: Athens, GA

Join Date: Apr 2012
Posts: 3
Default 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
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Old 07-08-2015, 09:00 AM   #2
GenoMax
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Location: East Coast USA

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Are you actually running (working on) a Proton sequencer or just using the data from a one?
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Old 07-08-2015, 09:33 AM   #3
avnairn
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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.
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Old 07-08-2015, 09:41 AM   #4
GenoMax
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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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Old 07-16-2015, 02:41 PM   #5
genehunter
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If you upgrade to torrent suite 4.6, there is a new RNA-Seq plugin with new plots, tables and downloadable tables.
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Old 07-17-2015, 10:51 AM   #6
avnairn
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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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