Paired-end & Mate-pair on PGM

[Findus]

Hi guys!
Now it's my time to ask for help of the Collective Mind of SeqAnswers.

The question is: Does anybody have experience with running PE or MP on PGM?

We've got som odd results with PE. Seems that we are loosing lots of beads during washings of the chip after finishing the first run. Has anybody encountered anything similar?

What are your impressions on PE on Ion Torrent? Is it useful at all with current read length?

What software would you recommend for PGM PE/MP analysis?

Many thanks in advance!

[Retro]

I would be also interested to know other people's experience with paired end runs and which software they use to analyze the data. When merging of individual paired reads is needed, I know only one program that can do that - NextGene from Softgenetics.

We have recently run a paired end amplicon sequencing run (200 bp from each end) and we can pair about 50% reads and successfully merge only about 25% reads.

[RonanC]

There's a thread over on the ion community board about this and it seems to me like people are not getting great results back from their paired end runs. IonTorrent are supposed to be coming out with a kit to do paired end runs later in the year so I think I'm going to wait until that comes out. No word on the release date though.