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Forum: Ion Torrent 10-12-2015, 06:49 AM
Replies: 37
Views: 52,497
Posted By Buzz0r
Hi guys, instead of going through the...

Hi guys,

instead of going through the trouble i would seriously consider to trial Illumina's new low input custom amplicon kit. That way you at least are using a standard optimised protocol with...
Forum: Ion Torrent 10-06-2014, 11:57 PM
Replies: 122
Views: 111,557
Posted By Buzz0r
lets see what comes new from IT on ASHG, I know...

lets see what comes new from IT on ASHG, I know Illumina will come with some more things but all of them have ben announced previously. Last thing i heard from a customer was that P2 will be around...
Forum: De novo discovery 03-18-2014, 06:56 AM
Replies: 4
Views: 2,545
Posted By Buzz0r
what is your average read length on the Proton. I...

what is your average read length on the Proton. I just saw some microbial data sets from a collaborator which clearly showed extreme improvement for the assemblies for the 2x300Bp reads on Miseq (avg...
Forum: Ion Torrent 01-07-2014, 10:07 PM
Replies: 122
Views: 111,557
Posted By Buzz0r
could post any links considering those avalanche...

could post any links considering those avalanche news or presetnations?
Forum: Ion Torrent 11-05-2013, 01:39 AM
Replies: 8
Views: 11,064
Posted By Buzz0r
In that case how can you compare the Qscores at...

In that case how can you compare the Qscores at all? Clearly, it makes a huge difference if you look at a Illumina Q30 run, a Proton Q17 run or a PacBio <Q10 run.

Just by looking at the data in a...
Forum: Ion Torrent 11-04-2013, 01:49 AM
Replies: 8
Views: 11,064
Posted By Buzz0r
Could you elaborate on how the Q30 (Ion) is !=...

Could you elaborate on how the Q30 (Ion) is != Q30 (Illumina)? I thought it is a set value showing an accuracy for base calling of 99.9% being correct (hence one error in 1000 bases).
Forum: Ion Torrent 06-27-2013, 01:53 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
Would be great to see some stats once you have...

Would be great to see some stats once you have some runs on. Thanks ...
Forum: Ion Torrent 06-27-2013, 01:42 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
Do you have a Proton in your lab in Thailand? How...

Do you have a Proton in your lab in Thailand? How is it performing?
Forum: Ion Torrent 06-26-2013, 08:06 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
it sounds great...and dreaming is fun (just...

it sounds great...and dreaming is fun (just thinking of water skiing with my own yacht) but I prefer things that are usable right now.
Forum: Ion Torrent 06-26-2013, 06:35 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
is that presentation online?

is that presentation online?
Forum: Ion Torrent 06-26-2013, 12:33 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
...another rumor! Fabulous... ^_^

...another rumor! Fabulous... ^_^
Forum: Ion Torrent 06-11-2013, 08:02 PM
Replies: 122
Views: 111,557
Posted By Buzz0r
...question is was it "on a table" at any time?...

...question is was it "on a table" at any time? ... tired of promises!
Forum: Ion Torrent 06-10-2013, 07:50 PM
Replies: 122
Views: 111,557
Posted By Buzz0r
Good morning, this is actually entertaining to...

Good morning,
this is actually entertaining to read with my morning cafe latte. You know you sound like Rothberg 1 year ago (actually this could be copy paste from one of their flyers probably)....
Forum: Ion Torrent 04-02-2013, 08:28 PM
Replies: 9
Views: 6,118
Posted By Buzz0r
Interesting, please keep us up to date on how you...

Interesting, please keep us up to date on how you progress in the Proton sample prep and the data metrics coming off the machine!

Any idea yet on how the quality looks of the data?

If you sift...
Forum: Core Facilities 04-02-2013, 08:23 PM
Replies: 18
Views: 11,832
Posted By Buzz0r
Hm, well good luck with the Proton! They keep...

Hm, well good luck with the Proton! They keep pushing the road maps and when you read what some of their advocates mention in interviews with experts and the lack of data of the Proton I see people...
Forum: Ion Torrent 03-22-2013, 12:04 AM
Replies: 122
Views: 111,557
Posted By Buzz0r
New skin for PGM? Did they only change the skin...

New skin for PGM? Did they only change the skin or did they also change some technical details of the PGM?

Are they trying to confuse you with the PGM and Proton skins now as they confuse you on...
Forum: Core Facilities 01-13-2013, 09:58 PM
Replies: 18
Views: 11,832
Posted By Buzz0r
it might be worth waiting till they actually can...

it might be worth waiting till they actually can produce some data..meanwhile the news from Illumina about new MISeq development in 2013 and the new Moleculo acquisition for long reads might be a...
Forum: Ion Torrent 12-13-2012, 08:23 PM
Replies: 6
Views: 3,512
Posted By Buzz0r
We are also looking for a public dataset for...

We are also looking for a public dataset for months now, quite annoyed we can not see what is really going on here!
Forum: Bioinformatics 12-10-2012, 03:50 AM
Replies: 7
Views: 6,697
Posted By Buzz0r
Hopefully, the plots generated by BaseSpace for...

Hopefully, the plots generated by BaseSpace for the MiSeq output will be exportable into plots soon, that might ease some of this extra effort a bit!
Forum: Bioinformatics 12-10-2012, 03:48 AM
Replies: 4
Views: 3,008
Posted By Buzz0r
you have the option to use BWA as an aligner in...

you have the option to use BWA as an aligner in the MiSeq workflow, have you tried this?
Forum: Bioinformatics 12-10-2012, 03:46 AM
Replies: 34
Views: 18,529
Posted By Buzz0r
FYI, Illumina already launched their own cloud...

FYI, Illumina already launched their own cloud solution called BaseSpace. It includes many 3rd party softwares and is opening up completely by the end of the year. Might be worth checking it out!
...
Forum: Illumina/Solexa 11-27-2012, 05:48 PM
Replies: 5
Views: 4,439
Posted By Buzz0r
Lightbulb Hi there,... what do you mean by "BaseSpace...

Hi there,...

what do you mean by "BaseSpace doesn't multiplex"? As far as i see it in my projects i can clearly see all different samples demultiplexed and even QC on the multiplexing so i wonder...
Forum: Bioinformatics 03-22-2011, 12:46 AM
Replies: 8
Views: 13,681
Posted By Buzz0r
Hi, i am also working with the standalone...

Hi,

i am also working with the standalone version x23 of P2.
we have some problems with it when lock files are not completely removed from the scratch library on our cluster. this will probably...
Forum: Bioinformatics 12-21-2010, 12:18 AM
Replies: 2
Views: 2,585
Posted By Buzz0r
a bit tricky since my files a re too big for...

a bit tricky since my files a re too big for excel to handle...did some command line stuff with awk and made another row with it but liftOver wont take it anyways since the format is not appreaciated...
Forum: Bioinformatics 12-19-2010, 09:20 PM
Replies: 2
Views: 2,585
Posted By Buzz0r
LiftOver for single positions

Hey,

does anyone know a tool to liftover form hg18 to hg19 for a file of the format:

#CHROM POS ID REF ALT QUAL FILTER INFO
1 533 . G C -1.0 0 AA=.;AC=6;AN=120;DP=423
...

problem is that...
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