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Search: Posts Made By: Chien-Yuan Chen
Forum: Bioinformatics 11-12-2009, 01:18 PM
Replies: 2
Views: 2,641
Posted By Chien-Yuan Chen
GEO data GSE 13652 Expression profiling by...

GEO data GSE 13652
Expression profiling by high throughput sequencing
We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice...
Forum: Literature Watch 11-09-2009, 02:36 PM
Replies: 0
Views: 2,123
Posted By Chien-Yuan Chen
ShortRead: a bioconductor package for input, quality assessment and exploration

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.

Program in...
Forum: Literature Watch 09-17-2009, 09:15 AM
Replies: 3
Views: 4,955
Posted By Chien-Yuan Chen
Improved Protocols for the Illumina Genome Analyzer Sequencing System

Improved Protocols for the Illumina Genome Analyzer Sequencing System

1: Curr Protoc Hum Genet. 2009 Jul;Chapter 18:Unit 18.2. Links
Improved protocols for the illumina genome analyzer sequencing...
Forum: Site Feedback/Suggestions 08-24-2009, 08:54 AM
Replies: 1
Views: 2,386
Posted By Chien-Yuan Chen
some suggestion

I have a suggestion, I do not know which is right or not. Because many biologists do not have computer background, they can not understand some bioinformatic tools and softwares. And many...
Forum: Literature Watch 08-07-2009, 07:15 AM
Replies: 0
Views: 2,209
Posted By Chien-Yuan Chen
Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome.

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome.

Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton...
Forum: Literature Watch 07-20-2009, 04:01 PM
Replies: 0
Views: 1,592
Posted By Chien-Yuan Chen
Mutation of FOXL2 in granulosa-cell tumors of the ovary.

N Engl J Med. 2009 Jun 25;360(26):2719-29. Epub 2009 Jun 10.

Mutation of FOXL2 in granulosa-cell tumors of the ovary.

It just published online by vancouver group. They found the novel gene...
Forum: Service Providers 06-23-2009, 02:41 PM
Replies: 11
Views: 14,647
Posted By Chien-Yuan Chen
We also spend 3 months to keep the quality better...

We also spend 3 months to keep the quality better in illumina GAII flowcells. Our initial problem is the cluster density too high, so the confluent cluster can not be interpretation. The second...
Forum: Illumina/Solexa 06-05-2009, 04:01 PM
Replies: 6
Views: 3,365
Posted By Chien-Yuan Chen
We cost about USD 1400 dollars per lane with...

We cost about USD 1400 dollars per lane with 75bpXII PE sequencing per lane.
Forum: Bioinformatics 06-02-2009, 11:43 AM
Replies: 2
Views: 2,784
Posted By Chien-Yuan Chen
Yes, we could find some lesions by pair end...

Yes, we could find some lesions by pair end sequencing, but I mean the method to get all the data at a time, not by check each lesion one by one.

Some commercial sofware such as CLC genome...
Forum: Bioinformatics 06-02-2009, 09:28 AM
Replies: 2
Views: 2,784
Posted By Chien-Yuan Chen
How do you find the insertion, deletion and translocation?

There are many tools can align genome /transcriptome.
But after alignment, how do you find these lesions such insertion deletion and translocation?

:confused:
Forum: Bioinformatics 05-27-2009, 12:35 PM
Replies: 14
Views: 4,633
Posted By Chien-Yuan Chen
If you use CLC genome workbench, the software can...

If you use CLC genome workbench, the software can manage this problem. But you should specify the insert length to prevent incorrect alignment.
Forum: Bioinformatics 04-17-2009, 10:25 AM
Replies: 0
Views: 1,297
Posted By Chien-Yuan Chen
Problems after alignment.....

Which methods can be used to approach a gene fusion after alignment in human genome?
Forum: Literature Watch 03-14-2009, 02:46 PM
Replies: 0
Views: 2,471
Posted By Chien-Yuan Chen
A pair end sequencing paper

:)Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1886-91.
Forum: Bioinformatics 03-07-2009, 11:49 AM
Replies: 0
Views: 1,651
Posted By Chien-Yuan Chen
Adequate coverage for genome wide pair end sequencing

For example a human genome, how many read and coverage may be adequate for pair end sequncing? By shear genomic DNA and mRNA?:confused:
Forum: General 03-04-2009, 08:54 AM
Replies: 0
Views: 1,595
Posted By Chien-Yuan Chen
Cost of next generation sequncing

Do You have any data about detail cost of single end sequncing, pair end sequncing? By illumina, 454 or other plateform.
Forum: RNA Sequencing 03-02-2009, 10:59 AM
Replies: 0
Views: 3,051
Posted By Chien-Yuan Chen
How many amounts of mRNA do you start the pair end sequencing?

How many amounts of mRNA do you start the pair end sequencing?

By the protocol, 10 ug RNA or 100ng mRNA will work. But by the published article, maybe 200 ng or more is necessary. It is not easy...
Forum: Illumina/Solexa 03-01-2009, 01:17 PM
Replies: 8
Views: 20,173
Posted By Chien-Yuan Chen
mate pair sequencing

Does Anybody has the experience of mate pair sequence? Except the insert size is different from pair end sequence, and what is the benefit with this method? :confused:
Forum: Illumina/Solexa 02-22-2009, 04:06 PM
Replies: 1
Views: 1,740
Posted By Chien-Yuan Chen
Yes, some reagent run out at the 10 th specimen

Yes, some reagent run out at the 10 th specimen
Forum: Introductions 02-14-2009, 11:21 AM
Replies: 0
Views: 1,401
Posted By Chien-Yuan Chen
Hello I am Chien-Yuan Chen

Hello I am Chien-Yuan Chen:):)
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