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Search: Posts Made By: Khen
Forum: General 11-26-2013, 02:06 PM
Replies: 42
Views: 12,708
Posted By Khen
Does anybody know about the relative acuracy of...

Does anybody know about the relative acuracy of the Illumina OmniExpress Plus? That is apparently what they use at 23andme but I have not seen any publications on this technology.
Forum: Pacific Biosciences 10-01-2013, 02:55 PM
Replies: 3
Views: 2,541
Posted By Khen
I suspect you will need a $%#@ ton more memory...

I suspect you will need a $%#@ ton more memory than 2 GB per 8 nodes. The cluster I use has 24GB per 12 cores and I wish I had twice as much memory.
Forum: General 09-06-2013, 02:23 PM
Replies: 3
Views: 2,217
Posted By Khen
I looked through the phase 1 data and could not...

I looked through the phase 1 data and could not find the rs numbers you provided. It may be the case that the variants in question were not observed in the 1000 genomes project. But really I have not...
Forum: General 09-06-2013, 12:23 PM
Replies: 3
Views: 2,217
Posted By Khen
Can you give an example?

Can you give an example?
Forum: General 05-15-2013, 10:15 PM
Replies: 27
Views: 7,218
Posted By Khen
For what its worth, I love my mac. I spent $1000...

For what its worth, I love my mac. I spent $1000 dollars on it almost 3 years ago and I wouldn't ditch it for anything but another apple product. IMHO, as far as laptops go, apple does a really good...
Forum: Bioinformatics 05-15-2013, 06:52 PM
Replies: 2
Views: 1,024
Posted By Khen
You could try dbGaP: ...

You could try dbGaP:
http://www.ncbi.nlm.nih.gov/gap
Access is restricted though, so you might have to get your PI to apply.
Forum: General 05-06-2013, 12:04 PM
Replies: 0
Views: 609
Posted By Khen
Best/favorite global pairwise alignment program for proteins

I need a global pairwise alignment program that I can invoke from a Java and run on my local machine. My problem is that I have had garbage collection issues with biojava's alignment packages when I...
Forum: Bioinformatics 04-29-2013, 01:11 PM
Replies: 20
Views: 3,882
Posted By Khen
Definitely need to find out what your scheduling...

Definitely need to find out what your scheduling software is. But in general, I prefer parallelization to multithreading. It is much easier and I find that I run into fewer problems.
Forum: Bioinformatics 04-07-2013, 04:55 PM
Replies: 5
Views: 1,202
Posted By Khen
Calling species B and C against the reference...

Calling species B and C against the reference together just saves space. And yes, you will still need to use the reference genome. The output is slightly different however, so what you will get is an...
Forum: Bioinformatics 02-10-2013, 07:15 PM
Replies: 0
Views: 465
Posted By Khen
Quality scores for the 1000genomes phase1 SNP call sets.

I am having trouble interpreting the genotype field from the 1000 genomes phase1 variant calls. My problem is that I donít know how to interpret the ĎGLí parameter in the genotype field. The VCF v4.1...
Forum: Bioinformatics 11-25-2012, 12:19 PM
Replies: 9
Views: 1,115
Posted By Khen
There is an example in the manual. ...

There is an example in the manual.

http://samtools.sourceforge.net/samtools.shtml
samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

The '-r' argument allows you to...
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