how to run command line

[lekgolwa.phalafala]

Hi,

I have just joined the forum and would like you to share your knowledge of bioinformatics with me. I am a student in plant molecular biology. My project focuses on the use of RNA-seq to study gene expression under osmotic stress.

Looking forward to engaging with you in the future

Cheers,
LP

[GenoMax]

Welcome!

Familiarize yourself with experimental design and basics of data analysis (if you are just starting to plan your project). Time investment up front can save you a lot of time/heartache down the road. Are you planning to analyze the data yourself or will you beworking with a collaborator?

[lekgolwa.phalafala]

Thanks GenoMax for welcoming me. You just raised some important points, and I am so thankful for that. Yes, I am going to analyse data myself since I do not have a collaborator, and I am completely new in the area of bioinformatics, let alone plant molecular biology. Anyway, it is the research field that I like, and I so wish that I do not run away when the going gets tough. So far, I have some Illumina RNA-seq data that I am busy trying to analyse using command line. I have already analysed the data a little bit using CLC Bio Genomics Workbench. I used the workbench to trim and map the reads to reference genome (Sbicolor v2.1). However, I have dropped the use of clc bio genomics workbench in favour of command line. I hope you guys will help me. I do not even know how to run command line.

[GenoMax]

Before you go any further spend a couple of days at this resource:http://korflab.ucdavis.edu/Unix_and_...ent.html#part1 It will help you become familiar with command line. These skills are going to be needed for pretty much anything you will be doing in terms of analysis.

Plant genomes are tough to work with (with ploidy etc). I am not familiar with sorgham but hopefully things are simpler than some other plant genomes.

Sounds like you are an experimental biologist. Getting good RNA and converting that into sound libraries is major part of the process. Data analysis, though important, will only come in play once you get good sequence data back.

[lekgolwa.phalafala]

Thank you very much GenoMax for the info you gave me. I will follow the link you provided, and I will try to understand as much information as possible. I never worked with RNA before nor the DNA, but what I have realised is that RNA (especially RNA from sorghum roots) is much more difficult to work with than DNA. The RNA-seq data I work with right now is from sorghum leaves, and it is just to give me an idea of what it is like to work with RNA sequencing and stuff. In my masters, I did nothing to do with RNA/DNA biology.