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Search: Posts Made By: lek2k
Forum: Ion Torrent 01-03-2012, 12:16 AM
Replies: 8
Views: 5,533
Posted By lek2k
We have ours connected to the UPS/Backup power...

We have ours connected to the UPS/Backup power point supplied by the Hospital we are based in. Unfortunately there is a split second delay before it kicks in which causes the Torrent Server to reboot...
Forum: Bioinformatics 11-03-2011, 06:10 PM
Replies: 5
Views: 3,959
Posted By lek2k
There is an example on the GATK website ...

There is an example on the GATK website
http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_command-line_arguments

Here's a direct link to the file if you don't wanna read all the text...
Forum: Ion Torrent 09-20-2011, 01:13 AM
Replies: 3
Views: 4,763
Posted By lek2k
Blog post shows what a difference software...

Blog post shows what a difference software improvements make in regards to throughput, speed and quality of analysis. Also shows the feasibility of the accuracy challenge.
...
Forum: Ion Torrent 09-20-2011, 01:11 AM
Replies: 9
Views: 5,318
Posted By lek2k
Yes that would be interesting for comparison....

Yes that would be interesting for comparison. I'll give it a go soon.
Forum: Ion Torrent 09-13-2011, 10:25 PM
Replies: 28
Views: 17,901
Posted By lek2k
wow I felt like a KGB agent reading that... I...

wow I felt like a KGB agent reading that... I mean pretending to know Russian :confused:
Forum: Ion Torrent 09-13-2011, 10:22 PM
Replies: 15
Views: 7,253
Posted By lek2k
Why FASTQ files and not the SFF files for Newbler...

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.
Forum: Ion Torrent 09-13-2011, 10:15 PM
Replies: 9
Views: 5,318
Posted By lek2k
Great EdgeBio blog post on Predicted vs Empirical...

Great EdgeBio blog post on Predicted vs Empirical QV and presents recalibration using GATK

http://www.edgebio.com/blog/?p=271
Forum: Ion Torrent 09-13-2011, 10:12 PM
Replies: 0
Views: 2,645
Posted By lek2k
Ion Torrent Accuracy Problem and Challenge - Non-technical explanation

This is mainly for people outside next-generation sequencing field and/or computer scientist.
...
Forum: Ion Torrent 09-04-2011, 11:19 PM
Replies: 9
Views: 5,318
Posted By lek2k
Broadly, this is how QVs are predicted using six...

Broadly, this is how QVs are predicted using six metrics and a phred lookup table. This is detailed in my latest blog post.
...
Forum: Ion Torrent 09-02-2011, 02:34 PM
Replies: 28
Views: 17,901
Posted By lek2k
Maybe they were passed around in presentations...

Maybe they were passed around in presentations during this week's road trip. Maybe someone managed to pocket one? :D
Forum: Ion Torrent 09-02-2011, 02:29 PM
Replies: 9
Views: 5,318
Posted By lek2k
Novoalign is not the official alignment program....

Novoalign is not the official alignment program. tmap is the official one created by Nils Homer so he would be the best to answer any questions on that.

Regarding QV calibration, I'm quite new to...
Forum: Ion Torrent 08-31-2011, 03:29 PM
Replies: 9
Views: 6,265
Posted By lek2k
Most have probably read this :cool: The blog...

Most have probably read this :cool:
The blog post on Genetic Future discusses the accuracy compared to the SoLiD.
...
Forum: Ion Torrent 08-31-2011, 03:12 PM
Replies: 18
Views: 22,551
Posted By lek2k
People, we need to say what the local currency...

People, we need to say what the local currency is. There is still a massive price difference after currency conversion. :confused:
Forum: Ion Torrent 08-31-2011, 02:43 PM
Replies: 18
Views: 10,492
Posted By lek2k
I'm going to go off memory on this one so please...

I'm going to go off memory on this one so please correct me if I'm wrong.

1. dephased reads may be lost for ever but the contributions they make exist. This is evident in a ionogram as the zeromer...
Forum: Ion Torrent 08-30-2011, 10:52 PM
Replies: 4
Views: 3,146
Posted By lek2k
Thanks ECO and Nils for the kind words and...

Thanks ECO and Nils for the kind words and encouragement. :D

I have updated my "About" Page. Hopefully people have a better feel for why I would spend a considerable amount of my time blogging....
Forum: Ion Torrent 08-29-2011, 10:33 PM
Replies: 4
Views: 3,146
Posted By lek2k
No problems. SEQanswers is the source of most of...

No problems. SEQanswers is the source of most of my blog hits. So of course I would publicize here.
Forum: Ion Torrent 08-29-2011, 09:42 PM
Replies: 4
Views: 3,146
Posted By lek2k
IonTorrent - The mathematics behind it all (blog series)

This is the first part of a blog series I'm writing. This has my mathematical interpretation behind the source code. Bring some water as it is very dry :D
But I put some pics in there :rolleyes:
...
Forum: Ion Torrent 08-29-2011, 07:25 PM
Replies: 9
Views: 5,318
Posted By lek2k
Smile Yes, a gapped alignment was used. Using the...

Yes, a gapped alignment was used. Using the following command line options
-g 20 -x5

which corresponds to a gap opening penalty of 20 and extension penalty of 5.
The default is -g 40, -x 15. ...
Forum: Ion Torrent 08-28-2011, 02:54 AM
Replies: 9
Views: 5,318
Posted By lek2k
Ion Torrent Rapid Accuracy Improvements (independent analysis)

The new blog series covers improvements over a 3 month time frame using the various data releases and includes in house PGM runs.
...
Forum: Ion Torrent 08-25-2011, 12:30 AM
Replies: 18
Views: 22,551
Posted By lek2k
Had a go last week. Didn't go so good for the 2%...

Had a go last week. Didn't go so good for the 2% size select gel :(
1. The gel had to be run much longer than in the instructions.
2. The water you put in the collection slots disappears quite...
Forum: Ion Torrent 08-22-2011, 12:31 AM
Replies: 0
Views: 2,763
Posted By lek2k
Challenges in Improving Ion Torrent Raw Accuracy

In this blog post I attempt to explicitly discuss what actually needs improving to improve on accuracy.
...
Forum: Sample Prep / Library Generation 08-18-2011, 06:32 PM
Replies: 2
Views: 2,509
Posted By lek2k
whoops my bad, wrong place. Yes, you should move...

whoops my bad, wrong place. Yes, you should move it. Thanks.
Forum: Ion Torrent 08-18-2011, 03:03 PM
Replies: 14
Views: 7,510
Posted By lek2k
Why don't you just elute in (treated) water to be...

Why don't you just elute in (treated) water to be on the safe side. If IonShear still doesn't work, you should run a NEB fragmentase experiment in parallel. Fragmentase is dirt cheap so worth a try.
Forum: Sample Prep / Library Generation 08-18-2011, 02:59 PM
Replies: 2
Views: 2,509
Posted By lek2k
Qiagen SeqTarget system - Don't go there friend !!

Just to let everyone know who are interested in the Qiagen SeqTarget system to think again if they want to buy this.
http://www.qiagen.com/products/seqtargetsystem.aspx

These are the reasons...
Forum: Ion Torrent 08-18-2011, 01:42 PM
Replies: 14
Views: 7,510
Posted By lek2k
You may also need a way of size selecting your...

You may also need a way of size selecting your fragments.
We are currently trialing the Invitrogen E-gel Size Select system. It's very fiddly but seems to do the job.
Showing results 1 to 25 of 32

 


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