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Search: Posts Made By: MrGuy
Forum: General 06-02-2014, 02:21 AM
Replies: 4
Views: 2,879
Posted By MrGuy
You are mixing up Revenues with Earnings. They...

You are mixing up Revenues with Earnings. They aren't the same thing. Revenue is the amount of money the company brought in. Earnings is the expenses (overhead, operations, R&D, etc) that are...
Forum: Ion Torrent 04-02-2014, 09:51 PM
Replies: 3
Views: 2,744
Posted By MrGuy
How did you do your size selection? How did you...

How did you do your size selection?
How did you quantify you library prior to OT2?
Are all your sequencing reagents fresh and from the same package?
Forum: Ion Torrent 03-20-2014, 10:23 AM
Replies: 13
Views: 7,211
Posted By MrGuy
ok, so it's: OT2+ES+chip loading --- 5-8 hours ...

ok, so it's:
OT2+ES+chip loading --- 5-8 hours
Isothermal+ES+chip loading -- 2 hours
Chef -- 10 hours for two chips
Sequencing still at 4 hours

In other words, with Chef, 18-20 hours would...
Forum: Ion Torrent 03-20-2014, 09:33 AM
Replies: 13
Views: 7,211
Posted By MrGuy
So, let me get this straight: you are saying...

So, let me get this straight: you are saying Ion's new sequencing chemistry will be sequencing SE 200 and 400 bp in 1 hour sequencing runs. Is that correct?
Forum: Ion Torrent 03-20-2014, 01:53 AM
Replies: 13
Views: 7,211
Posted By MrGuy
what read length? PE?

what read length? PE?
Forum: Genomic Resequencing 03-05-2014, 05:02 AM
Replies: 1
Views: 1,639
Posted By MrGuy
Optimize your PCRs in singleplex to give the same...

Optimize your PCRs in singleplex to give the same peak height and same mastermix/thermalcycling program. Then pool the non-overlapping amplicons in one tube, then the others in another tube. Step...
Forum: Ion Torrent 12-12-2013, 07:25 AM
Replies: 6
Views: 6,223
Posted By MrGuy
Here's their marketing guy talking about it: ...

Here's their marketing guy talking about it:
http://www.yuzuki.org/ion-chef-pii-chip-isothermal-template-prep-and-a-new-hi-q-enzyme-at-ion-world-2013/

Synopsis for those who don't want to click:...
Forum: Ion Torrent 09-17-2013, 12:31 AM
Replies: 5
Views: 4,595
Posted By MrGuy
The only question is if they are v1 or v2. v1 is...

The only question is if they are v1 or v2. v1 is more or less worthless unless you are running short sequences or doing training exercises. The v2 are worth something. 314 chips are only a...
Forum: Ion Torrent 06-13-2013, 02:27 AM
Replies: 9
Views: 6,266
Posted By MrGuy
You could probably suggest to the sequencing...

You could probably suggest to the sequencing center to have them install a plug in called PathogenAnalyzer. It's on the community. It looks to me to be designed specifically for viral/bacterial...
Forum: Ion Torrent 05-28-2013, 03:46 AM
Replies: 4
Views: 3,171
Posted By MrGuy
So, just ran a long amplicon. ~425 bp with 75%...

So, just ran a long amplicon. ~425 bp with 75% of reads over Q20 at the last base.
Forum: Illumina/Solexa 05-02-2013, 10:33 PM
Replies: 58
Views: 37,768
Posted By MrGuy
Even getting a single read of something errant is...

Even getting a single read of something errant is enough to shut. down. everything. Thus having even the slightest risk of detectable contamination means having proper controls in place to properly...
Forum: Ion Torrent 05-02-2013, 10:25 PM
Replies: 4
Views: 3,171
Posted By MrGuy
We're in the early stages of the 400bp chemistry,...

We're in the early stages of the 400bp chemistry, so not too much to definitively say at this point. Regardless, we are looking into the similiarity issue and created something to look at reads as...
Forum: Ion Torrent 04-29-2013, 12:19 AM
Replies: 4
Views: 3,171
Posted By MrGuy
I've been doing some work with amplicons in that...

I've been doing some work with amplicons in that range. Some mixed populations work, some not. Essentially the error profile is improved, you get the entire amplicon, reads drop off towards the end....
Forum: Bioinformatics 04-24-2013, 12:36 AM
Replies: 4
Views: 7,038
Posted By MrGuy
TMAP works very well. Bowtie pretty bad. CLC...

TMAP works very well. Bowtie pretty bad. CLC (commercial) worked just as good as TMAP. Mosaic worked fine, too. I generally find if you follow the manufacturers recommendations things seem to work...
Forum: Metagenomics 04-24-2013, 12:24 AM
Replies: 4
Views: 3,214
Posted By MrGuy
That enzyme will work fine. I don't think we'll...

That enzyme will work fine. I don't think we'll ever buy a sonicator.
Forum: Metagenomics 04-23-2013, 11:13 PM
Replies: 4
Views: 3,214
Posted By MrGuy
It depends on what you are trying to do. If you...

It depends on what you are trying to do. If you want to retain strandedness, then I'd suggest tagging individual molecules, fragmenting, sequence, reassemble, then get on with the analysis. I...
Forum: SOLiD 04-18-2013, 06:25 AM
Replies: 6
Views: 2,091
Posted By MrGuy
We're just using Ion Shear. We haven't seen any...

We're just using Ion Shear. We haven't seen any notable artifacts so far, but we only use it occasionally. I think we are up to 40 genomes on it, many of which were replicats or nearly identical...
Forum: Ion Torrent 04-15-2013, 06:15 AM
Replies: 70
Views: 20,485
Posted By MrGuy
Maybe spun off to Roche? Or sold to Illumina? :D

Maybe spun off to Roche? Or sold to Illumina? :D
Forum: Ion Torrent 04-15-2013, 05:59 AM
Replies: 70
Views: 20,485
Posted By MrGuy
Well, seems Thermo bought them. ...

Well, seems Thermo bought them.

http://finance.yahoo.com/news/thermo-fisher-buy-life-technologies-120801466.html
Forum: SOLiD 04-11-2013, 01:02 AM
Replies: 6
Views: 2,091
Posted By MrGuy
We have one and it works as advertised. It...

We have one and it works as advertised. It obviates the need of a lot of other equipment when short on budget -- bioanalyzer, shearing tool, size selection. It takes about 2.5 hrs to run. Some...
Forum: Ion Torrent 03-20-2013, 05:46 AM
Replies: 4
Views: 6,417
Posted By MrGuy
I actually find the NGS lab workflow for the...

I actually find the NGS lab workflow for the instrumentation not important. Most of the time I spend is gathering the samples and designing experiments rather than digitizing them. A roche Jr could...
Forum: The Pipeline 02-21-2013, 10:07 PM
Replies: 19
Views: 22,877
Posted By MrGuy
Some little bird told me starlight is alive.

Some little bird told me starlight is alive.
Forum: Ion Torrent 01-31-2013, 10:05 PM
Replies: 4
Views: 5,905
Posted By MrGuy
No experience yet as we are getting through our...

No experience yet as we are getting through our old kits first. The v2 will start being used once the 400 kits are available.
Forum: Sample Prep / Library Generation 01-27-2013, 10:05 PM
Replies: 46
Views: 21,940
Posted By MrGuy
Ampure isn't very stringent. I see a lot of...

Ampure isn't very stringent. I see a lot of small fragments left over that get in the way. For now, I'm using pre-cast gels that have a precast well to suck out your sample. It's not precise in the...
Forum: Ion Torrent 12-17-2012, 11:50 PM
Replies: 4
Views: 5,905
Posted By MrGuy
We just unpacked ours. Seems it is a...

We just unpacked ours. Seems it is a thermalcycler based instrument, so no gas is needed to drive fluids. What's nice is now the sequencer and the thermalcycler are completely separate now. The v2...
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