SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to analyze RNA-seq data ? bioR RNA Sequencing 3 09-12-2013 08:08 AM
what is the best software to use to analyze illumina NGS data? bbsinfo Illumina/Solexa 3 08-21-2013 05:48 AM
DEXSeq - able to analyze paired (matched) data? spabinger RNA Sequencing 13 02-08-2012 11:40 AM
New Tools to analyze Next Gen Seq data JMFA Bioinformatics 0 12-02-2010 09:26 AM
any one use grape to analyze solexa data zhidong Bioinformatics 11 05-22-2009 12:07 AM

Reply
 
Thread Tools
Old 09-06-2012, 07:06 AM   #1
farrel75
Member
 
Location: MI

Join Date: May 2012
Posts: 11
Default What's your favorite way to analyze your data?

So imagine I have a FASTA file from my assembly run on the Miseq. As I am completely unfamiliar with anything to do with downstream analysis or the various software, I don't know what to do with the data. So...what's your favorite thing to do with it? What should I do? I assume I need to put all the reads together somehow. So please fill me with your knowledge oh wise ones!
farrel75 is offline   Reply With Quote
Old 09-06-2012, 12:35 PM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

ABySS.

But there are other genome sequencers as well. Some tuned to different branches of life; e.g., those oriented towards bacterial assembly.

I suggest reading the forum. Lots of information in it.
westerman is offline   Reply With Quote
Old 09-08-2012, 05:40 AM   #3
Mark
Member
 
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 51
Default

While redirecting it to /dev/null will save you alot of disk space and headaches, it may upset the PI.
Your question is much too vague. Define the purpose of the study then seek out tools.
Mark is offline   Reply With Quote
Old 09-09-2012, 07:34 AM   #4
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

Every analysis should be a goal and I choose programs that fits to it. What is your aim?
TiborNagy is offline   Reply With Quote
Old 09-09-2012, 10:54 AM   #5
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

Quote:
Originally Posted by Mark View Post
While redirecting it to /dev/null will save you alot of disk space and headaches, it may upset the PI.
Your question is much too vague. Define the purpose of the study then seek out tools.
A great suggestion especially for those that do not know why they did an experiment in the first place...
adaptivegenome is offline   Reply With Quote
Old 09-10-2012, 07:07 AM   #6
farrel75
Member
 
Location: MI

Join Date: May 2012
Posts: 11
Default

To be fair, I wasn't too sure of the goal myself. What we did was whole genome sequencing with a lot of genomes (E. coli, L. reuterii, and C. difficile). This was more of a trial thing to try out the MiSeq so there wasn't really a goal involved. Basically, I'm supposed to run it and play with the data to figure out what I can do with it.

I guess the questions are what is a good assembler for bacterial genomes? Right now I'm playing around with Velvet but I want to see what else is out there. So does anyone have any suggestions on what I could try out?

Also, anyone a big fan of mapping and wanting to rave about their favorite program for it?
farrel75 is offline   Reply With Quote
Old 09-14-2012, 03:03 AM   #7
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

I like MIRA for assembling bacterial genomes, because it has some hybrid assembling methods.
TiborNagy is offline   Reply With Quote
Old 09-14-2012, 04:04 AM   #8
Mark
Member
 
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 51
Default

Why don't you start with the MiSeq's onboard analysis tools (velvet, BWA, etc) , then move to the standalone version's of these to see what the increased ability to parameterize these tools can do for you, and then perhaps move on to other tools.
Mark is offline   Reply With Quote
Reply

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 05:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO