PEMer with Illumina?

[jkersh]

Has anyone run the PEMer workflow using Illumina data? I have been looking through the documentation and have created the conversion file from the Maq output, but there doesn't seem to be much information on how to use that file within the workflow.

We have PEMer installed so I wanted to run it to compare with Breakdancer, but so far it has been a hassle since it isn't very obvious how to work with the Illumina data, any help is appreciated.

Thanks!

[shruti]

Hi.. I was looking for some help in this regard as well..
did you happen to use it.
Would be nice if you could share some information.
Thanks

[Irsan_Kooi]

Hi there,

I have the same situation, illumina paired end reads, have run breakdancer and want to compare results with pemer. I think i have managed to get it to work, it is running now for half a day. Are you still interested in sharing some thoughts about this? We can do a audio/video meeting and help share our screens.

Cheers