SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Do I have to install velvet twice to run color and base space? pepperoni Bioinformatics 4 03-06-2012 10:32 AM
Color-space/SOLID assembly issues? JueFish Bioinformatics 19 12-14-2011 05:21 AM
Problems with mapping SOLID color space sequences to hg19 using TopHat davidehs Bioinformatics 1 06-24-2011 02:21 PM
Solid formats translator(base space/color space/double encoded) AronaldJ SOLiD 0 10-26-2010 12:10 AM
direct mapping of color-space data against color-space begsch SOLiD 1 09-09-2009 09:25 PM

Reply
 
Thread Tools
Old 06-13-2012, 04:56 AM   #1
pepperoni
Member
 
Location: US

Join Date: Oct 2011
Posts: 59
Default Columbus, Velvet color space SOLiD support

Hello, I want to assemble de novo SOLiD data with velvet but with fasta and sam references. Does anyone know if Columbus from Velvet supports color space? and how should I use it? shall I put the reference file in color or base space and the .sam/.bam file in color or base space?
thanks
pepperoni is offline   Reply With Quote
Old 06-13-2012, 01:06 PM   #2
pepperoni
Member
 
Location: US

Join Date: Oct 2011
Posts: 59
Default

I wrote to D. Zerbino, velvet's author, directly. He told me that to date Columbus does not support color space.
Any suggestions to assemble de novo with SOLiD data but with a fasta/.sam/.bam reference?
pepperoni is offline   Reply With Quote
Old 06-14-2012, 02:55 AM   #3
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
Default

If nothing is available, you could always convert to base space. I know, it's not recommended, but if the software is lacking.

One group developing software for SOLiD (metagenome) assembly is the Armbrust lab. It may be interesting to look at their work, Seastar, as it progresses.
colindaven is offline   Reply With Quote
Old 06-19-2012, 04:18 AM   #4
pepperoni
Member
 
Location: US

Join Date: Oct 2011
Posts: 59
Default

thanks conlindaven
pepperoni is offline   Reply With Quote
Reply

Tags
color space, columbus, de novo assembly, solid, velvet

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 10:55 PM.


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