SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
Color-space mapping with Bowtie ikarus97 Bioinformatics 3 06-30-2011 08:56 AM
Converting nucleotide-space to color-space javijevi Bioinformatics 7 11-29-2010 02:14 AM
junction mapping in color space Uwe Appelt Bioinformatics 19 10-26-2010 06:14 AM
Solid formats translator(base space/color space/double encoded) AronaldJ SOLiD 0 10-26-2010 12:10 AM
Comparison of mapping program performance for color-space reads? g_solid SOLiD 12 04-27-2010 01:11 PM

Reply
 
Thread Tools
Old 09-09-2009, 01:43 AM   #1
begsch
Junior Member
 
Location: France

Join Date: Jul 2009
Posts: 7
Cool direct mapping of color-space data against color-space

Hi,

I would like to know if someone has already tried to map color-space reads against other reads in color-space. The mapper of CoronaLite does not have an option for this - therefore I am at the moment analysing the source code for picking the necessary function (since at some point the reference genome has to be transfered in csfasta format and then further processed). Are there any other solutions for such an analysis?

I will keep you updated.

Regards,
begsch
begsch is offline   Reply With Quote
Old 09-09-2009, 09:25 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by begsch View Post
Hi,

I would like to know if someone has already tried to map color-space reads against other reads in color-space. The mapper of CoronaLite does not have an option for this - therefore I am at the moment analysing the source code for picking the necessary function (since at some point the reference genome has to be transfered in csfasta format and then further processed). Are there any other solutions for such an analysis?

I will keep you updated.

Regards,
begsch
You can create a multi-fasta reference, where each "contig" is a read. Just translate the color-space reference into nucleotide space and run a color-space aware aligner (which will re-convert your reference into color space). Remember to retain the adaptor. Color space aligners include BFAST, BWA, MAQ, MOSAIK, SHRIMP, SOCS, ZOOM, ...

Nils
nilshomer 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 11:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO