Introduction

[avnairn]

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

[GenoMax]

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

[avnairn]

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.

[GenoMax]

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

[genehunter]

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

[avnairn]

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!