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Forum: Academic/Non-Profit Jobs 04-11-2012, 06:57 AM
Replies: 0
Views: 1,605
Posted By Nix
Bioinformatics Data Analyst/ Programmer I/II - Salt Lake City, UT

Job Summary
The Bioinformatics Shared Resources (BSR) at the University of Utah (http://bioserver.hci.utah.edu) seeks a Bioinformatics Data Analyst (I or II)
to consult with world class...
Forum: Bioinformatics 04-07-2011, 01:19 PM
Replies: 1
Views: 1,479
Posted By Nix
Capture design for snp sequencing

Has anyone though about how to best design capture probes (we're using Agilent's Custom SureSelect) for sequencing candidate SNPs?

If one designs the probe centered over the SNP then the greatest...
Forum: Bioinformatics 02-21-2011, 07:39 AM
Replies: 82
Views: 30,549
Posted By Nix
DAS servers are web apps and as such can take...

DAS servers are web apps and as such can take advantage of the same security protocols worked out for banks and hospitals (ssl, https, digest authentication, vpn). With our GenoPub server, visibility...
Forum: Bioinformatics 02-18-2011, 02:37 PM
Replies: 82
Views: 30,549
Posted By Nix
Funny you should mention this. I've shared many...

Funny you should mention this. I've shared many a beer with librarians over a campfire and they are very keen on doing just this sort of thing. They are way into the proper annotation and curation...
Forum: Bioinformatics 02-18-2011, 01:26 PM
Replies: 82
Views: 30,549
Posted By Nix
The problem with both of these approaches is the...

The problem with both of these approaches is the lack of a formal language to associate annotation with the data. Species, genome version, file format are often anyone's guess. Every group encodes...
Forum: Bioinformatics 02-18-2011, 11:52 AM
Replies: 82
Views: 30,549
Posted By Nix
If your group can run a web site it can run a...

If your group can run a web site it can run a DAS/2 server. It really is rather easy to set up, just mysql and tomcat. Then have the biologists use the point and click web interface to load the...
Forum: Bioinformatics 02-18-2011, 10:44 AM
Replies: 82
Views: 30,549
Posted By Nix
Smile DAS/2 to the rescue?!

Why aren't people hosting and publishing their own data? There's no need to centralize this activity.

You are responsible for providing plasmids and cell lines etc. used in your papers why not...
Forum: Bioinformatics 01-14-2011, 12:14 PM
Replies: 6
Views: 2,247
Posted By Nix
Wasn't aware Colin and crew were building such...

Wasn't aware Colin and crew were building such tools! Will check them out.

I've built a variety of apps for processing novoalign bisulfite reads, single end or paired into the USeq package. (See...
Forum: Illumina/Solexa 10-04-2010, 05:53 PM
Replies: 4
Views: 4,412
Posted By Nix
We (Huntsman Cancer Institute) just published a...

We (Huntsman Cancer Institute) just published a paper describing a Genomic LIMS and Analysis Project Center called GNomEx. It's free/ open source, supports microarray and next gen sequencing...
Forum: Bioinformatics 09-24-2010, 02:34 PM
Replies: 4
Views: 2,814
Posted By Nix
SNP and INDEL callers for novoalign or SAM?

Hello Folks,

I was wondering what people are using to call SNPs and INDELS from novoalign alignments? I've been converting to maq and using that package but was wondering if anything else is...
Forum: Events / Conferences 08-26-2010, 09:25 AM
Replies: 6
Views: 8,265
Posted By Nix
Can this be accessed afterward for US folks or...

Can this be accessed afterward for US folks or repeated? 3AM is a bit early.
Forum: Bioinformatics 08-07-2010, 05:28 AM
Replies: 3
Views: 3,293
Posted By Nix
Hmm, 36bp is sufficient for chIP-seq, shoot...

Hmm,

36bp is sufficient for chIP-seq, shoot for >10-20 million duplicate free uniquely mapped reads (1/2 - 1 lane on a GAIIx), and at minimum provide 5ng of correctly sized chIP product to your...
Forum: Bioinformatics 07-30-2010, 12:57 PM
Replies: 6
Views: 2,448
Posted By Nix
Check out http://useq.sourceforge.net/ and the...

Check out http://useq.sourceforge.net/ and the user guide describing differential transcriptome analysis http://useq.sourceforge.net/usage.html .
Forum: Sample Prep / Library Generation 07-08-2010, 10:04 AM
Replies: 10
Views: 4,604
Posted By Nix
NGSfan, If you don't mind my asking, what...

NGSfan,

If you don't mind my asking, what read coverage rates are you seeing for the ccds exons at your various sequencing depths? (e.g. what % of the ccds exons are covered by 8 or more reads at...
Forum: Bioinformatics 06-11-2010, 06:12 AM
Replies: 2
Views: 1,417
Posted By Nix
I'd recommend letting the data tell you how many...

I'd recommend letting the data tell you how many peaks you have. Use an app that controls for overdispersion and calls p-values using say a negative binomial distribution and also control for...
Forum: Bioinformatics 03-18-2010, 06:32 AM
Replies: 32
Views: 33,827
Posted By Nix
Yes, I've built a rather sophisticated tool for...

Yes, I've built a rather sophisticated tool for doing just this sort of thing. See IntersectRegions in the USeq package.
...
Forum: Bioinformatics 03-16-2010, 06:16 AM
Replies: 32
Views: 33,827
Posted By Nix
Hello Gonghong, Yes, Novoalign is it's own...

Hello Gonghong,

Yes, Novoalign is it's own beast (an excellent one at that) and is from Novocraft. So first run your reads through their aligner and then process your data with USeq. For...
Forum: Bioinformatics 02-22-2010, 07:43 AM
Replies: 43
Views: 20,311
Posted By Nix
OK. It's good to have all of these choices in...

OK. It's good to have all of these choices in visualizations. Lots of cross pollination. I know the GenoViz folks (I'm one too but don't work on IGB directly) are looking at how you've implemented...
Forum: Bioinformatics 02-22-2010, 07:25 AM
Replies: 43
Views: 20,311
Posted By Nix
Igb

I use IGB extensively for RNA-Seq visualizations, both paired and single reads, read coverage graphs, and for window enrichment analysis. It's quite exceptional and has parsers for most of the...
Forum: Bioinformatics 02-07-2010, 05:24 AM
Replies: 48
Views: 51,299
Posted By Nix
Yes I did try Picard's SAMFileReader but it has a...

Yes I did try Picard's SAMFileReader but it has a major memory management problem when trying to parse RNA-Seq data that contains alignments to chromosomes and splice junctions. These alignment...
Forum: Bioinformatics 02-06-2010, 09:01 AM
Replies: 48
Views: 51,299
Posted By Nix
OK, 4hrs later and I can parse the strand..... ...

OK, 4hrs later and I can parse the strand.....

Here's some java code so folks don't have to go through this again:

<pre>
/**
* Index Index^2 MethodName Flag DescriptionFromSamSpec
*...
Forum: Bioinformatics 02-05-2010, 12:53 PM
Replies: 48
Views: 51,299
Posted By Nix
Wow, the more I dig into sam the more it looks...

Wow, the more I dig into sam the more it looks like a horse put together by a committee. These bit flags are ridiculous for a human readable text alignment format.
Forum: Bioinformatics 02-03-2010, 07:49 AM
Replies: 32
Views: 33,827
Posted By Nix
There are a lot of files associated with the...

There are a lot of files associated with the results. I also wanted this archived so follow the link above and download the README_Report.doc.zip file for the summary.
Forum: Bioinformatics 01-28-2010, 05:05 AM
Replies: 9
Views: 6,182
Posted By Nix
USeq does differential RNA-Seq

Check out the USeq package. http://useq.sourceforge.net

I've added functionality to look for changes in expression and structure for known genes (no novel discovery) using binomial and...
Forum: Epigenetics 11-18-2009, 10:22 AM
Replies: 20
Views: 63,244
Posted By Nix
Here's the thread to the ChIP Seq Challenge...

Here's the thread to the ChIP Seq Challenge http://seqanswers.com/forums/showthread.php?t=1039
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