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Forum: Genomic Resequencing 11-04-2014, 07:56 PM
Replies: 0
Views: 1,657
Posted By mkeehan
A union of alleles file for glia

Does anyone have suggestions for generating the union of alleles file that is fed into glia to perform realignment for freebayes.

I am trying to build a ensemble variant detection pipeline.
I...
Forum: Bioinformatics 10-19-2010, 07:03 PM
Replies: 11
Views: 3,233
Posted By mkeehan
Try seqan from http://www.seqan.de It's really...

Try seqan from http://www.seqan.de
It's really good.
Forum: Bioinformatics 10-10-2010, 04:13 PM
Replies: 1
Views: 1,256
Posted By mkeehan
actual use of GPGPUs

Is anyone actually successfully using GPGPU based hardware for next Gen Sequencing use?

I've heard of one organisation using GPU-HMMER but is there anyone using a GPGPU package for short read...
Forum: Bioinformatics 07-21-2010, 03:02 PM
Replies: 6
Views: 1,861
Posted By mkeehan
Are you still using your system with 16GB of RAM?...

Are you still using your system with 16GB of RAM?
You are probably swapping if it's using 19GB...

I found reading the manual to get the right parameters made a huge difference to the reads per...
Forum: Bioinformatics 06-30-2010, 06:53 PM
Replies: 2
Views: 1,816
Posted By mkeehan
recommendations on disk storage infrastructure

Hi
We are planning the IT for our sequencing project. We are expecting to sequence half a dozen dairy bulls (Bos Taurus) at 30 times coverage a year for the next few years. I plan to thoroughly...
Forum: Bioinformatics 06-23-2010, 05:15 PM
Replies: 5
Views: 1,945
Posted By mkeehan
I found this on "split-read" mapping ...

I found this on "split-read" mapping

http://seqanswers.com/forums/archive/index.php/t-2267.html
Forum: Bioinformatics 06-23-2010, 02:47 PM
Replies: 5
Views: 1,945
Posted By mkeehan
MosaikAligner is my favourite hammer. ...

MosaikAligner is my favourite hammer.
http://bioinformatics.bc.edu/marthlab/Mosaik

But it seems that you want to do overlap based alignment scoring.
It might require a custom script and...
Forum: Bioinformatics 05-17-2010, 01:58 PM
Replies: 9
Views: 3,521
Posted By mkeehan
8 controls and 8 cases just like an early...

8 controls and 8 cases just like an early micro-array experiment.
Consult a statistician to diagnose how much power was in the experiment.
Then report the species of the bacterial genomes in the...
Forum: Events / Conferences 04-12-2010, 01:23 PM
Replies: 4
Views: 4,993
Posted By mkeehan
Has any information on the "Cortex de...

Has any information on the "Cortex de Bruijn-based assembly and variant-calling framework" been made public? It sounds very useful!
Forum: General 03-09-2010, 12:20 PM
Replies: 5
Views: 3,455
Posted By mkeehan
Done! I've put the reference in for the rates...

Done! I've put the reference in for the rates I've quoted.
Forum: General 03-09-2010, 11:22 AM
Replies: 5
Views: 3,455
Posted By mkeehan
I've tentatively added two rows for the...

I've tentatively added two rows for the technology average read error rate. Any suggestions on a comprehensive error study rather than relying on the initial papers for each technology?
Forum: Introductions 02-02-2010, 12:10 PM
Replies: 373
Views: 143,564
Posted By mkeehan
Gidday, My name is Mike, I work for LIC, a...

Gidday,

My name is Mike, I work for LIC, a dairy breeding cooperative in Hamilton, New Zealand. We use sequence data to breed better dairy bulls for pastoral based dairy farmers throughout the...
Forum: Bioinformatics 02-02-2010, 12:04 PM
Replies: 4
Views: 2,639
Posted By mkeehan
My jump database was about 20 GB in size. Having...

My jump database was about 20 GB in size. Having that all in memory is much faster than swapping to disk. So I'd go for the large memory but it really depends on the size of the jump database you...
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