consed and illumina paired ends

[ggloor]

Has anyone been able to get the phrap/phred/consed package to show paired end reads generated with Illumina/Solexa technology. We are able to get our reads mapped onto our contigs, but there is no paired end information imported.

The consed manual is not very clear on how to do this.

We would like to be able to validate our contigs before finishing the annotations

Thanks

[Torst]

Has anyone been able to get the phrap/phred/consed package to show paired end reads generated with Illumina/Solexa technology. We are able to get our reads mapped onto our contigs, but there is no paired end information imported.

I don't think consed can show "links" between pairs. It just shows reads and their orientation. The phred/phrap/consed package comes with a tool called "phrapview" which can examine the pairing on a genome-wide scale.