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Old 07-29-2011, 06:06 AM   #1
nickloman
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Default Early experiences with 316 chips

Shameless plug for my blog post:
http://pathogenomics.bham.ac.uk/blog...t-impressions/

But genuinely interested to discuss with any other users of 316 chips how they find their quality profiles.
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Old 08-01-2011, 04:40 AM   #2
drmrgd
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I wonder...have you run a 314 chip with the new upgrades for the 316 chip and compared to a 314 chip run with the old flow rate? I'm wondering if the increased error rate is strictly related to the chip or the new fluidics calibration. We're about to get the upgrade, and now I'm a little bit panicky about it. We've not seen very good error rate results up to this point to begin with!
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Old 08-01-2011, 08:00 AM   #3
nickloman
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We haven't run the 314 since having the fluidics upgrade - I agree it would be interesting to see what the results are.
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Old 08-02-2011, 06:40 AM   #4
arolfe
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Default 314 after upgrade

We've run 314 chips after the fluidics upgrade (in fact, we haven't run any 316 chips yet) and haven't seen anything substantially different. Like Nick, the new software produces quality scores that are more uniform along the length of the read.

Alex
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Old 08-03-2011, 09:14 AM   #5
drmrgd
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Thanks for the info! The consistency over the length of the read is nice. But, the overall drop is not something we're interested in. We're finding all kinds of sequencing errors and problems with our data, and have actually redesigned some of our amplicons to take advantage of the early, higher quality reads.
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Old 09-09-2011, 05:10 PM   #6
SamH
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What happened when you ran Ion Torrent FASTQ files through Newbler 2.6? It seems like it is handling some fastq files I fed it okay... but am I in for a bad surprise when the assembly finishes?

Sam
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Old 09-13-2011, 09:22 PM   #7
lek2k
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Why FASTQ files and not the SFF files for Newbler 2.6?
I ran Newbler on all my Ion Torrent SFF files and the metrics look similar to the ones posted by Nick and Lex on their blogs.
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Old 10-22-2011, 07:39 PM   #8
seq_me
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Thumbs up Seq analysis time difference

Thanks for the informative article. I was wondering what is difference in processing time for sequence analysis for the 314, 316 and 318 chips.
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Old 11-17-2011, 05:47 AM   #9
soleulloa
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Hi all,

I'm preparing our first run using 316, but I'm not sure if I have to use the same "user guide" that we used for 314 preparation.
Is there any changes in protocols for 316?
Please, help me!!!

Thanks in advance

Soledad
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Old 11-17-2011, 05:58 AM   #10
nickloman
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Best thing to do is to read the documentation on the Ion Torrent community and check for sure:
http://lifetech-it.hosted.jivesoftware.com/index.jspa
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Old 11-17-2011, 06:02 AM   #11
soleulloa
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Hi nickloman,

Thanks for your early response!
I've being looking for Ion Community, but I can't find information about this

I need someone that was performed 316 runs... pleaaaaase!!!
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Old 11-17-2011, 06:26 AM   #12
nickloman
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Have a look at http://lifetech-it.hosted.jivesoftwa.../docs/DOC-1803 - you can see there are differences between 314 and 316 protocol.
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Old 11-17-2011, 06:31 AM   #13
soleulloa
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Wowwwwww thank you so much!!!!

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Old 11-27-2011, 11:33 PM   #14
singaporeseq
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Default Experience with multiplexing on ion torrent?

Has anyone seen any protocols for multiplexing on ion torrent? I can't find a protocol anywhere. Has anybody done this/ used the barcode kit?
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Old 06-21-2012, 05:02 AM   #15
Silvia Weidner
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We would like to buy an Ion Torrent PGM Sequencer in our institute.
Does anyone have some experiences with this Sequencer?
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Old 06-25-2012, 08:17 PM   #16
ECO
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Quote:
Originally Posted by singaporeseq View Post
Has anyone seen any protocols for multiplexing on ion torrent? I can't find a protocol anywhere. Has anybody done this/ used the barcode kit?
Quote:
Originally Posted by Silvia Weidner View Post
We would like to buy an Ion Torrent PGM Sequencer in our institute.
Does anyone have some experiences with this Sequencer?
Please make new threads for these questions.
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