SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SHRiMP alignment results for colorspace miRNA dsidote Bioinformatics 2 11-10-2011 10:32 AM
Tophat with colorspace zorph RNA Sequencing 1 11-08-2010 10:54 AM
Alignment Visualization kwtennis311 Bioinformatics 5 06-17-2010 12:04 AM
MAQ - colorspace alignment troubles Jonathan Bioinformatics 1 01-20-2010 11:16 PM
sam output from bwa colorspace alignment Mr Mutundes Bioinformatics 0 12-15-2009 04:02 AM

Reply
 
Thread Tools
Old 05-10-2010, 12:35 AM   #1
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default Colorspace alignment visualization

Hi Community,

I am not entirely satisfied with what's available for whole-genome browsing of color space alignments.

I have tried IGV and had a look at the SOLiD alignment browser but I have run into some problems

I have a sorted BAM file from BFAST and I'm not sure how to change this to the Bioscope GFF3 format.

Has anybody had better luck in properly displaying colorspace alignments to a reference genome? I would like to see SNPs, sequencing errors, etc. in colorspace as compared to the reference sequence.
zee is offline   Reply With Quote
Old 05-10-2010, 07:36 AM   #2
lvaruzza
Junior Member
 
Location: Brazil

Join Date: Feb 2008
Posts: 8
Default

You can open the sorted BAM file in IGV (http://www.broadinstitute.org/igv/)
lvaruzza is offline   Reply With Quote
Old 05-10-2010, 07:36 PM   #3
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

I've been using IGV all this time. It works fine although what I mean is that I would like to be able to view the actual base-pair detail at the highest resolution.
Perhaps it is the structure of my BAM file but I guess I will need to consult the IGV support team if it is an issue.
zee is offline   Reply With Quote
Old 05-11-2010, 06:05 AM   #4
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

Probably not want you are looking for since it's commercial but CLCBio's Genomic Workbench shows the basepair detail, original color space call and quality values in the alignment contigs.
NextGenSeq is offline   Reply With Quote
Old 05-11-2010, 06:54 PM   #5
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

Thanks NextGenSeq. That is exactly what I'm looking for but I guess not in a commercial package

Quote:
Originally Posted by NextGenSeq View Post
Probably not want you are looking for since it's commercial but CLCBio's Genomic Workbench shows the basepair detail, original color space call and quality values in the alignment contigs.
zee is offline   Reply With Quote
Old 05-12-2010, 11:47 AM   #6
martian_bob
Member
 
Location: New York

Join Date: Feb 2010
Posts: 11
Default

Are you willing to do a bit of programming? You can view the BAM file in SAM format (see the manual), send the output to a file, run a program to decode the colorspace bits, and then go from there...
martian_bob 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 09:56 AM.


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