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Forum: Literature Watch 07-12-2017, 10:22 PM
Replies: 1
Views: 7,723
Posted By tedwong
Metagenome sequins (spike-in controls)

Dear Sequencing Community,

We have just released a new set of sequins that represent a synthetic microbe community, and act as reference standards for use in metagenome applications.

Metagenome...
Forum: Bioinformatics 01-11-2017, 10:09 PM
Replies: 1
Views: 1,621
Posted By tedwong
Why should MA plot be flat after normalization?

I'm talking about the slide: http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/ma08_bw.pdf

In page 5, the title is "Why is Normalization an Issue?". The author compares the MA plot...
Forum: Literature Watch 09-21-2016, 02:26 AM
Replies: 7
Views: 10,349
Posted By tedwong
Dear All, We have now launched our website...

Dear All,

We have now launched our website at www.sequin.xyz

Here, you can access useful resources and information on sequins. For those of you who are now starting to return sequencing...
Forum: Literature Watch 08-16-2016, 06:34 PM
Replies: 7
Views: 10,349
Posted By tedwong
Hi Devon, no we have not done any de novo...

Hi Devon, no we have not done any de novo assembly with Trinity. Our existing data could definitely be used to assess transcriptome reconstruction with Trinity, e.g. to measure sensitivity and...
Forum: Literature Watch 08-15-2016, 12:45 AM
Replies: 7
Views: 10,349
Posted By tedwong
Thanks. Feel free to post any questions here. We...

Thanks. Feel free to post any questions here. We will also release a software framework for the sequins very soon, and how sequins can be used in bioinformatics.
Forum: Literature Watch 08-14-2016, 07:57 PM
Replies: 3
Views: 8,734
Posted By tedwong
We have started a formal thread for current and...

We have started a formal thread for current and future users to discuss DNA sequins:

http://seqanswers.com/forums/showthread.php?p=197786#post197786

or RNA sequins:
...
Forum: Literature Watch 08-14-2016, 07:51 PM
Replies: 7
Views: 10,349
Posted By tedwong
Sequins: spike-in standards for RNA sequencing

RNA sequencing (RNA-seq) has become a central tool with wide-ranging research and clinical applications. However, accurate resolution of gene expression is confounded by the sheer size and complexity...
Forum: Literature Watch 08-14-2016, 06:52 PM
Replies: 3
Views: 8,734
Posted By tedwong
Hi nucacidhunter, DNA sequins can be used...

Hi nucacidhunter,

DNA sequins can be used with any sequencing platform. An application where the combination of long-read sequencing (eg PacBio) and Sequins will be particularly powerful is in the...
Forum: Literature Watch 08-14-2016, 06:40 PM
Replies: 0
Views: 7,588
Posted By tedwong
Sequins: spike-in standards for genome sequencing

Genome sequencing has become a principal tool in biomedical research and clinical diagnostics. However, numerous experimental and bioinformatic variables influence the sensitivity and precision of...
Forum: Bioinformatics 07-14-2016, 12:54 AM
Replies: 26
Views: 16,765
Posted By tedwong
I'm using Cufflinks 2.2.1 but still seeing...

I'm using Cufflinks 2.2.1 but still seeing duplicate genes in the tracking file. Has the issue ever fixed?
Forum: Bioinformatics 03-19-2015, 05:49 PM
Replies: 4
Views: 3,418
Posted By tedwong
Parse CIGAR string in C/C++

What'd be the best way to parse a CIGAR string fully according to the specification in C/C++? Would regular expression work?
Forum: Bioinformatics 03-10-2015, 11:54 PM
Replies: 0
Views: 1,167
Posted By tedwong
Problem compile cufflinks on Xcode

I have installed all requirements for compiling cufflinks. I'm compiling the sources with their provided Xcode project.

Everything goes well but during the linking phase:

ld: warning: directory...
Forum: Bioinformatics 03-03-2015, 09:01 PM
Replies: 1
Views: 1,556
Posted By tedwong
Beginner Questions

I'm a beginner to the field. I'm trying to align my reads to a reference genome. However, I'm not quite sure I understand what tophat is trying to do. In fact, I want to make sure my understanding to...
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