SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
paired-end vs. mate-pair lre1234 Bioinformatics 8 04-05-2013 06:25 AM
Samtools Flag to identify outward facing (mate-pair not paired end) reads lesander Bioinformatics 5 10-28-2011 02:24 PM
Are the mate-pair reads always shadowed by their friends the paired-end (picture) seb567 Illumina/Solexa 1 07-15-2011 10:49 AM
exon capture & mate-pair: Which order? rstarke Sample Prep / Library Generation 4 02-16-2011 08:51 AM
Difference between mate pair and pair end bassu General 2 06-19-2010 07:13 AM

Reply
 
Thread Tools
Old 03-16-2012, 01:24 AM   #1
Findus
Junior Member
 
Location: Uppsala, Sweden

Join Date: Feb 2012
Posts: 2
Default Paired-end & Mate-pair on PGM

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!
Findus is offline   Reply With Quote
Old 06-29-2012, 08:00 AM   #2
Retro
Member
 
Location: Pennsylvania

Join Date: Apr 2011
Posts: 27
Default

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.
Retro is offline   Reply With Quote
Old 07-11-2012, 10:37 AM   #3
RonanC
Junior Member
 
Location: USA

Join Date: Jul 2012
Posts: 8
Default

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.
RonanC is offline   Reply With Quote
Reply

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 03:31 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO