SEQanswers

Go Back   SEQanswers > Applications Forums > Genomic Resequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
CLC Genomics Workbench - Windows vs. Linux figure002 Bioinformatics 24 12-06-2013 06:10 AM
CLC Genomics Workbench ECO Bioinformatics 65 03-27-2012 04:05 AM
CLC Genomics Workbench for de novo RNA-seq JQH Bioinformatics 1 07-12-2011 11:17 PM
CLC Genomics Workbench goes hand in hand with Ion Torrent data CLC bio Vendor Forum 0 05-12-2011 05:34 AM
Mapping RNA seq using CLC Genomics WOrkbench rururara Bioinformatics 1 02-22-2011 11:35 AM

Reply
 
Thread Tools
Old 10-15-2010, 06:45 AM   #1
Dapip33
Junior Member
 
Location: Boston, MA

Join Date: Feb 2010
Posts: 5
Default Getting a full annotation onto a consensus sequence in CLC Genomics Workbench

Hi all,

I'm having a little problem with my analysis using CLC tools. I am trying to assemble illumina reads from clinical isolates of P. aeruginosa and do SNP analysis between strains that have evolved overtime. My problem is that I can do the assemblies just fine against a reference genome or de novo, but I cannot get good annotation files to do SNP analysis. Here's my procedure:

1. Assemble the early strain against annotated reference genome. Copy the annotations onto the consensus sequence and save that as my Early genome.
2. Assemble the late strain against the Early genome, and then do SNP report.
3. Get SNP report and realize that the most useful comparator data in the SNP table is not there, specifically the PAxxx gene numbers used in updated Pseudomonas annotations (www.pseudomonas.com).

When I look at the consensus sequence copied over from step #1, it looks like the PAxxx numbers are there, but the SNP report and the assembly in step 2 does not include them. Anybody know how to get the full annotation from a reference genome onto a consensus in CLC Genomics Work bench?

Last edited by ECO; 10-15-2010 at 06:46 AM. Reason: Fixed typo in link
Dapip33 is offline   Reply With Quote
Old 09-19-2013, 07:02 AM   #2
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 227
Default

Quote:
Originally Posted by Dapip33 View Post
Hi all,

I'm having a little problem with my analysis using CLC tools. I am trying to assemble illumina reads from clinical isolates of P. aeruginosa and do SNP analysis between strains that have evolved overtime. My problem is that I can do the assemblies just fine against a reference genome or de novo, but I cannot get good annotation files to do SNP analysis. Here's my procedure:

1. Assemble the early strain against annotated reference genome. Copy the annotations onto the consensus sequence and save that as my Early genome.
2. Assemble the late strain against the Early genome, and then do SNP report.
3. Get SNP report and realize that the most useful comparator data in the SNP table is not there, specifically the PAxxx gene numbers used in updated Pseudomonas annotations (www.pseudomonas.com).

When I look at the consensus sequence copied over from step #1, it looks like the PAxxx numbers are there, but the SNP report and the assembly in step 2 does not include them. Anybody know how to get the full annotation from a reference genome onto a consensus in CLC Genomics Work bench?
I'd ask the company (CLC) directly - sometimes export options are obvious in the CLC products.
cement_head is offline   Reply With Quote
Reply

Tags
annotation, clc

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 04:36 AM.


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