Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Analysis of viral amplicons with hypervariable regions Mr Jefferson 454 Pyrosequencing 3 12-23-2012 09:12 AM
Old dog needs to learn new tricks stefanloliver Introductions 0 06-29-2012 01:52 PM
PubMed: Structural and functional analysis of viral siRNAs. Newsbot! Literature Watch 0 04-07-2010 03:00 AM
Size Selection Tricks?? wiggy 454 Pyrosequencing 0 06-18-2009 11:11 AM

Thread Tools
Old 11-20-2013, 03:44 PM   #1
Junior Member
Location: College Station, TX

Join Date: Nov 2013
Posts: 1
Question Viral Qausispecies analysis- tips and tricks? PLEASE HELP!

So my project, which was NOT supposed to be bioinformatic, has turned into a bioinformatics things.
Does ANYONE here have suggestions on how to best quantify and analyze viral quasispecies subpopulations?
And, full disclosure, I am HORRIBLE at programming. I learn quick, but it is not a strong skill for me.
I can't find a GUI interface for any of the quasispecies software. So ANY help on coding and how to make things run and run easier would be greatly appreciated.
So any comments? VisPa? QuRe? I have tried just running Samtools SNP caller, but it says I don't have any variants....but I do. Because I can see them in CLC. i just don't know how to make CLC give me the information. Plus CLC is so resource intensive it keeps crashing out on me.
CrazyCoV is offline   Reply With Quote
Old 11-20-2013, 09:49 PM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

I recommend harrassing CLC support until you get your money's worth out of that software; just relax and let them do the coding side of things for you. If it costs as much as an entry-level bioinformatician to run, you should really be able to survive without any bioinformatics skills to use it and interpret the results.

On a lighter note...
Does ANYONE here have suggestions on how to best quantify and analyze viral quasispecies subpopulations?
I'm not familiar with how all the buzzwords you've used relate to the railway station, but you might get a better response by using the magic word "metagenomics". A brief search on the goggle brings up the following webber:

Maybe that will be useful for you? I've seen it mentioned on SeqAnswers a bit, but am not familiar enough with metagenomics to say whether or not it would be good. Unfortunately, anything metagenomic is going to need bioinformatics skills and a bit of paper reading.
gringer is offline   Reply With Quote
Old 11-22-2013, 03:02 AM   #3
Location: London, UK

Join Date: Feb 2012
Posts: 25

I think you're probably going to need a slightly more specialist tool than CLC to get you through this.

I suggest you also look over ShoRAH (Zagordi(2011)Bioinformatics) and V-Phaser (Macalalad(2012)PLoS Comp Biol).
A.N.Other is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:32 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO