Getting a full annotation onto a consensus sequence in CLC Genomics Workbench

[Dapip33]

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?

[cement_head]

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.