Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to use Talbet to visualise bam file xinhaiping Bioinformatics 1 06-13-2011 02:18 PM
Pileup shows variants - Not called as SNPs BertieWooster Bioinformatics 10 05-12-2011 11:57 AM
SNPs detection from NGS data slakov Bioinformatics 0 03-15-2011 05:34 AM
Visualise SNPs with IGV boetsie Bioinformatics 1 01-21-2011 04:11 AM
How to visualise alignments with different read lengths? lindseyjane Bioinformatics 5 09-17-2009 02:27 AM

Thread Tools
Old 01-12-2011, 10:21 AM   #1
Junior Member
Location: Nottingham

Join Date: Oct 2010
Posts: 9
Default Softwear to visualise snps called from NGS

I used DeepSeq to identify novel SNPs in targeted amplicon regions. I have annotated these SNPs using variant classifier. However, I am yet to find a tool that can graphically display these SNPs in their genomic context. I was wondering if their is a stand alone tool, or perhaps something as part of a pipeline programme i can tap into? Anyone know of any?
mrxcm3 is offline   Reply With Quote
Old 01-13-2011, 02:07 AM   #2
Location: Planet Earth

Join Date: Jan 2011
Posts: 26

You can use custom tracks in the UCSC Genome Browser.
You can also setup a local installation of this, if you prefer this.
doc.ramses is offline   Reply With Quote
Old 01-13-2011, 11:56 AM   #3
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Not my field, but is Flapjack relevant?
maubp is offline   Reply With Quote
Old 01-14-2011, 12:25 PM   #4
Location: Canada

Join Date: Nov 2008
Posts: 37

I really like the Integrative Genomics Browser lately:
Jean is offline   Reply With Quote

genome, image, snp, visualization

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 07:28 AM.

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