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Search: Posts Made By: adamyao
Forum: Bioinformatics 09-07-2015, 05:30 PM
Replies: 5
Views: 2,697
Posted By adamyao
If you have pair end fastq.gz files, you can...

If you have pair end fastq.gz files, you can directly upload them to HiPipe (http://hipipe.ncgm.sinica.edu.tw/) for exome analysis. HiPipe driven by high performance computing has a few...
Forum: Bioinformatics 10-16-2014, 05:41 PM
Replies: 7
Views: 7,877
Posted By adamyao
Sambamba (http://lomereiter.github.io/sambamba/)...

Sambamba (http://lomereiter.github.io/sambamba/) provides some useful multi-threaded utilities like view, sort, mark duplicate, etc. We have taken advantage of this to speed up our process.
Forum: Bioinformatics 08-27-2014, 05:41 PM
Replies: 3
Views: 1,251
Posted By adamyao
You can try to upload your vcf file to VarioWatch...

You can try to upload your vcf file to VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do?mega=true) to see if the annotation can be done.
Forum: Bioinformatics 12-04-2013, 04:10 PM
Replies: 5
Views: 4,329
Posted By adamyao
If you have pair-end fastq files you can upload...

If you have pair-end fastq files you can upload them to HiPipe directly (http://hipipe.ncgm.sinica.edu.tw/). HiPipe powered by 640 cores can do alignment (BWA) and variant calling (GATK) very fast. A...
Forum: Bioinformatics 11-24-2013, 04:22 PM
Replies: 5
Views: 7,118
Posted By adamyao
Online annotation tool VarioWatch...

Online annotation tool VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/) capable of annotating millions of variants in minutes should be a good candidate to satisfy your expectation.
Forum: Bioinformatics 11-21-2013, 03:41 PM
Replies: 13
Views: 5,959
Posted By adamyao
Try to get as much ram as possible especially...

Try to get as much ram as possible especially when you want to open many windows in Partek.
Forum: Bioinformatics 09-17-2013, 09:59 PM
Replies: 11
Views: 11,861
Posted By adamyao
20.8G bases (104M reads, Pair End) 1 node (16...

20.8G bases (104M reads, Pair End) 1 node (16 cores) AMD 2.4GHz 96G ram
- 28 hours
Tophat 2 runs best with 16 cores ( single node) according to our tests otherwise it takes longer.
STAR runs...
Forum: Bioinformatics 01-16-2013, 07:56 PM
Replies: 6
Views: 3,226
Posted By adamyao
My lab members have recorded memory consumption...

My lab members have recorded memory consumption by TopHat-fusion. The following is the outcome

4 million pair-end reads (100bp read length):
Max memory used: 10G

88 million:
Max memory used:...
Forum: Bioinformatics 10-31-2012, 11:47 PM
Replies: 3
Views: 2,638
Posted By adamyao
I had this problem before. I tried two different...

I had this problem before. I tried two different ways: to increase memory and to use single thread. My machines are 32GB and 128GB. The 32GB always gets error (out of memory) on whole human genome...
Forum: Bioinformatics 10-04-2012, 11:48 PM
Replies: 12
Views: 4,404
Posted By adamyao
I had the same problem. My boost 1.51.0 library...

I had the same problem.
My boost 1.51.0 library was located in /home/adam/Downloads/lib
I did the following to solve the problem before installing TopHat:
...
Forum: Bioinformatics 08-20-2012, 06:39 PM
Replies: 3
Views: 1,745
Posted By adamyao
VarioWatch...

VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) provides visual output up to one thousand variants online in real time. It also provides text output for millions of variants....
Forum: Bioinformatics 08-20-2012, 06:29 PM
Replies: 5
Views: 2,140
Posted By adamyao
You can try VarioWatch...

You can try VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do). It should be able to provide what you want with graphical output in real time. By using "Query by Bacth" can give you...
Forum: Bioinformatics 07-26-2012, 11:57 PM
Replies: 2
Views: 1,409
Posted By adamyao
For annotation tool with GUI, there are some. One...

For annotation tool with GUI, there are some. One of them is VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch). It provides online real time annotation on millions of variants in just a few...
Forum: Bioinformatics 07-16-2012, 08:50 PM
Replies: 7
Views: 7,563
Posted By adamyao
Alternatively, direct upload your vcf to...

Alternatively, direct upload your vcf to MegaQuery of VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do?mega=true) should receive your results online in real time.
Forum: Bioinformatics 12-05-2011, 12:12 AM
Replies: 4
Views: 5,013
Posted By adamyao
Dear kiradi, You can try VarioWatch...

Dear kiradi,

You can try VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) to see if it helps. It provides MegaQuery Download to download millions of annotated variants for NGS...
Forum: Bioinformatics 10-05-2011, 12:31 AM
Replies: 3
Views: 3,032
Posted By adamyao
For variant annotation of human genome, would you...

For variant annotation of human genome, would you like to try using VarioWatch to see it fits your needs.
http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do

Adam
Forum: Introductions 02-16-2011, 03:48 AM
Replies: 4
Views: 1,306
Posted By adamyao
Taiwan is hot in summer and has typhoons. We...

Taiwan is hot in summer and has typhoons. We started to utilize NGS for translational research since last year though having more experience in genotyping arrays.
Forum: Introductions 02-15-2011, 04:42 AM
Replies: 4
Views: 1,306
Posted By adamyao
Wink Hi, are you coming back to Taipei soon?

Hi, are you coming back to Taipei soon?
Forum: Introductions 02-11-2011, 05:50 AM
Replies: 4
Views: 1,306
Posted By adamyao
Smile Hi, I am from Taipei.

Bioinformatics is my work focus. Nice to exchange experience and learn from you.
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