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Forum: Ion Torrent 12-12-2013, 08:29 AM
Replies: 6
Views: 5,835
Posted By IonTorrent
Regarding the latest updates on a few key product...

Regarding the latest updates on a few key product innovation areas (Ion Chef, Isothermal Amplification, Hi-Q sequencing chemistry, Ion PII Chip), please take a look at these two Ion World...
Forum: Ion Torrent 12-09-2013, 09:13 AM
Replies: 5
Views: 3,209
Posted By IonTorrent
Hi there, After logging in to the AmpliSeq...

Hi there,

After logging in to the AmpliSeq Designer website (https://ampliseq.com/), navigate to the Ion Panels page. From there you can choose to 'Download panel files" for the panel you need....
Forum: Ion Torrent 11-08-2013, 01:17 PM
Replies: 7
Views: 4,635
Posted By IonTorrent
Sorry, we might have missed the earlier post....

Sorry, we might have missed the earlier post. Please do consider Ion Community for those kinds of requests as well - there are team members monitoring the various spaces who are dedicated to...
Forum: Ion Torrent 11-08-2013, 08:00 AM
Replies: 7
Views: 4,635
Posted By IonTorrent
Hi there GenoMax, In fact, Torrent Suite...

Hi there GenoMax,

In fact, Torrent Suite software (and a few other packages) is open source and is freely available via our github repository:
https://github.com/iontorrent

As mentioned on the...
Forum: Ion Torrent 10-08-2013, 10:36 AM
Replies: 2
Views: 2,318
Posted By IonTorrent
Hi there, At the present we have the 16...

Hi there,

At the present we have the 16 barcode kit available for RNA. Please send me a private message and I would be happy to share information of how we might be able to assist with your need.
Forum: Ion Torrent 09-13-2013, 06:26 AM
Replies: 3
Views: 4,923
Posted By IonTorrent
Hi there, There is functionality within the...

Hi there,

There is functionality within the Torrent Suite software for duplicate read marking, which can be enabled as desired. There is more information available via the Help tool within Torrent...
Forum: Ion Torrent 09-09-2013, 12:57 PM
Replies: 1
Views: 4,716
Posted By IonTorrent
Hi there, "Switch" Solution is simply meant...

Hi there,

"Switch" Solution is simply meant to convey the change in conditions between the PCR and ligation steps of the library construction workflow.

For what it's worth, SEQanswers is an...
Forum: Ion Torrent 08-29-2013, 09:21 AM
Replies: 2
Views: 4,575
Posted By IonTorrent
Hi there, In our experience, off-target...

Hi there,

In our experience, off-target reads are typically a combination of specific per panel and per sample effects. For example, the best HMW DNAs will tend to have very similar off-target...
Forum: Ion Torrent 08-22-2013, 08:31 AM
Replies: 17
Views: 10,237
Posted By IonTorrent
Hi there, If you are an Ion Torrent...

Hi there,

If you are an Ion Torrent customer, the documentation for Torrent Suite may be found linked within Torrent Browser. For others, or for offline access, the relevant documents are also...
Forum: Ion Torrent 08-22-2013, 08:00 AM
Replies: 6
Views: 6,468
Posted By IonTorrent
Hi there, Ion Community is completely open...

Hi there,

Ion Community is completely open to all registrants - i.e. there are no member access levels. You should have full access to all technical information contained within.

With the...
Forum: Ion Torrent 07-23-2013, 12:16 PM
Replies: 6
Views: 6,468
Posted By IonTorrent
Hi there, There are, in fact, two library...

Hi there,

There are, in fact, two library adaptors - we call them A and P1. In most library preparations these are ligated onto library insert fragments. In some cases, these may be amplified onto...
Forum: Ion Torrent 06-14-2013, 07:26 AM
Replies: 121
Views: 99,820
Posted By IonTorrent
Hi there, The information you heard at AACR...

Hi there,

The information you heard at AACR is incorrect. As previously announced, the Avalanche chemistry is on track to be launched in 2013
Forum: Ion Torrent 05-09-2013, 06:26 PM
Replies: 3
Views: 2,676
Posted By IonTorrent
Hi Brandon, While there's not an official...

Hi Brandon,

While there's not an official supported protocol to do that with MuSeek, you're absolutely correct - full length ds cDNA can generally be treated like gDNA for most library prep...
Forum: Ion Torrent 03-01-2013, 03:38 PM
Replies: 27
Views: 15,180
Posted By IonTorrent
Hi Alessandro, TMAP is open source:...

Hi Alessandro,

TMAP is open source: https://github.com/iontorrent/TMAP

Also, if you were unable to access the link posted by jdilts, you can register for an account at the Ion Community...
Forum: Ion Torrent 01-22-2013, 06:28 AM
Replies: 9
Views: 3,027
Posted By IonTorrent
Hi Véronique, What method of poly(A)...

Hi Véronique,

What method of poly(A) enrichment did you use? Is this a human RNA sample? What you describe generally has its roots in the initial RNA enrichment/depletion, as opposed to the...
Forum: Metagenomics 01-11-2013, 09:35 AM
Replies: 3
Views: 2,052
Posted By IonTorrent
I believe those represent IUPAC nucleotide...

I believe those represent IUPAC nucleotide ambiguity codes:
http://www.bioinformatics.org/sms/iupac.html

H = A, C, or T
V = A, C, or G
W = A or T
Forum: Ion Torrent 12-07-2012, 06:49 AM
Replies: 6
Views: 4,425
Posted By IonTorrent
Hi Joltex, Regarding the adaptor...

Hi Joltex,

Regarding the adaptor concentration in the kit- for the kits supported by the current Ion Xpress Plus Fragment Library Preparation User Guide...
Forum: Ion Torrent 12-07-2012, 06:20 AM
Replies: 2
Views: 3,612
Posted By IonTorrent
Hi Apex, Libraries for the Ion Proton...

Hi Apex,

Libraries for the Ion Proton Sequencer are indeed made using the same adaptors presently used on Ion PGM Sequencer. This means that you can sequence PGM libraries via the OneTouch 2 and...
Forum: Ion Torrent 11-16-2012, 08:28 AM
Replies: 3
Views: 1,967
Posted By IonTorrent
Hi soleulloa, I've attached an image of the...

Hi soleulloa,

I've attached an image of the current library table. which highlights the target insert size for each sequencing read length. Parameters for the 400 base read methods will be added...
Forum: Ion Torrent 09-27-2012, 12:00 PM
Replies: 17
Views: 9,863
Posted By IonTorrent
Avalanche is not Wildfire.

Avalanche is not Wildfire.
Forum: Ion Torrent 08-27-2012, 07:36 AM
Replies: 1
Views: 1,415
Posted By IonTorrent
Hello JWJH, Have you considered an AmpliSeq...

Hello JWJH,

Have you considered an AmpliSeq custom panels...
Forum: Ion Torrent 08-20-2012, 06:56 AM
Replies: 8
Views: 6,168
Posted By IonTorrent
Hi there, Indeed, this does seem unusual and...

Hi there,

Indeed, this does seem unusual and I'd like to help you with your question. I tried to send you a follow up note but your profile settings do not seem to allow receipt of messages from...
Forum: Ion Torrent 08-08-2012, 07:17 AM
Replies: 4
Views: 7,327
Posted By IonTorrent
Hi Apex, The sequences of the fragment...

Hi Apex,

The sequences of the fragment library adaptors can be found in Appendix D (pp. 45) of the current Ion Xpress™ Plus gDNA Fragment Library Preparation User Guide...
Forum: Ion Torrent 07-18-2012, 03:14 AM
Replies: 10
Views: 10,595
Posted By IonTorrent
Hi slm1816, Thanks for reporting the issue...

Hi slm1816,

Thanks for reporting the issue with the KRAS G12D exon number in Ion Reporter™ Software. We confirmed this error recently and have identified a solution. You can expect an update...
Forum: Ion Torrent 07-05-2012, 02:26 PM
Replies: 27
Views: 15,180
Posted By IonTorrent
Hi hengnck, Are you using all 480 Mbp of...

Hi hengnck,

Are you using all 480 Mbp of data in the assembly or are you downsampling? I ask because many software packages (like those you mention) will grossly underperform with excessive...
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