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BioCode's Notes: July 2015

http://computationalproteomic.blogspot.com/2015_07_01_archive.html

Computational Proteomics and Bioinformatics. Monday, 27 July 2015. One big lesson I just learn. The picture completely changed, after one year abroad, the only big think I learned is that outside my farm and my small country: time, ideas, contacts are gold. In science you have people with you can work and collaborate, because they are open by nature (not only because they source code is in github. Monday, July 27, 2015. Subscribe to: Posts (Atom). Recently Published Proteomics Manuscripts. Every day, I e...

mendeliandisorder.blogspot.com

Mendelian Disorder: December 2011

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Genomics . bioinformatics . biotechnology . sequencing . opinions. Friday, December 9, 2011. Perhaps because it changes too often, GATK's available annotations for VCF files does not seem to be online anywhere that I've seen. The GATK site says to run GATK with the "- list" parameter to list them. Doing that requires putting in valid input files and such. Basically, it's a pain. So here's the list from GATK v1.3-21-gcb284ee. Available annotations for the VCF INFO field:. Links to this post.

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Mendelian Disorder: February 2012

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Genomics . bioinformatics . biotechnology . sequencing . opinions. Friday, February 17, 2012. I just posted a thread. On 23andMe about which annotations I use for my exome data. Here's what I said:. The annotations I've been including are:. Gene annotation (type of mutation- exonic, intronic, splicing, etc.). Mutational description (i.e. specific amino acid change, etc.). WashU Exome Variant DB (EVS). Transcription Factor Binding Site (TFBS). PolyPhen 2 score (PP2). The idea behind these types of annotat...

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Mendelian Disorder: ASGH2012 Fail

http://mendeliandisorder.blogspot.com/2012/10/asgh2012-fail.html

Genomics . bioinformatics . biotechnology . sequencing . opinions. Wednesday, October 31, 2012. Encouraging cloning by putting multiple highly interesting talks I want to see in concurrent sessions. twitter.com/mjcgenetics/st…. Mdash; Michael James Clark (@mjcgenetics) October 31, 2012. Subscribe to: Post Comments (Atom). View my complete profile. Misunderstood: Genetic tests and the people who do. Performance comparison of whole-genome sequencing platforms. Color Brewer 2.0.

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Mendelian Disorder: Sequencing My Exome: Why?

http://mendeliandisorder.blogspot.com/2012/02/sequencing-my-exome-why.html

Genomics . bioinformatics . biotechnology . sequencing . opinions. Friday, February 10, 2012. Sequencing My Exome: Why? 8220;Why do you want to do this? My wife, immediately after I tell her I'm going to sequence my own exome. There are a few times in life where you want to do something so badly, but find it difficult to convey to others why. I could frame a whole dissertation on the reasons behind wanting to sequence my own exome. (And I will.) But first, the simple answer:. And to do that, first you&#8...

mendeliandisorder.blogspot.com

Mendelian Disorder: May 2012

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Genomics . bioinformatics . biotechnology . sequencing . opinions. Friday, May 11, 2012. ANNOVAR Patching (May 11, 2012). Add support for Feb 1kG release. It turns out I had made a typo in the command and the Feb 2012 variants work fine! Just be very careful to have it as "1000g2012feb all" in the annotation part. Fix to 1kG annotation confusion. But line 136 in the annotate variation.pl script enforces a naming scheme that doesn't match this. Rather, one would need to use "1000g2011may all. Not sure wha...

mendeliandisorder.blogspot.com

Mendelian Disorder: whoami

http://mendeliandisorder.blogspot.com/p/whoami.html

Genomics . bioinformatics . biotechnology . sequencing . opinions. Me with a Complete Genomics sequencing chip. Put your nanoballs in the little lanes and watch them go! Michael James Clark, Ph.D. Human genetics, genomics, bioinformatics. Recently, I had my own genotypes run by 23andMe and have been excited to dive into that data. I intend to share my results, thoughts, and analyses of my own data as I go. And yes, someday soon I plan to sequence myself! Subscribe to: Posts (Atom). Color Brewer 2.0.

mendeliandisorder.blogspot.com

Mendelian Disorder: Where have I been?

http://mendeliandisorder.blogspot.com/2013/01/where-have-i-been.html

Genomics . bioinformatics . biotechnology . sequencing . opinions. Monday, January 21, 2013. Where have I been? I was never someone who blogged a great deal. But once or twice a month, I would put hand to keyboard and come up with something to talk about that is relevant to my favorite field of study: Genetics. I have every intention to continue doing that. But last April I started working for a small start-up company, and I've been very busy. I tried writing a grant once where I had planned out ten year...

computationalproteomic.blogspot.com

BioCode's Notes: first tweet with more than 1k rt and my post with more than 5k

http://computationalproteomic.blogspot.com/2015/06/first-twit-with-more-than-1k-rt-and-my.html

Computational Proteomics and Bioinformatics. Monday, 8 June 2015. First tweet with more than 1k rt and my post with more than 5k. Happy to see my first post with more than 5k visits:. Introduction to Feature selection for bioinformaticians using R, correlation matrix filters, PCA and backward selection. And my first tweet with more than 1k RTs:. Brilliant pic.twitter.com/dvOUhUb5k6. 8212; Yasset Perez-Riverol (@ypriverol) May 26, 2015. Thanks to my Readers. Monday, June 08, 2015. Where is the information?

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Mendelian Disorder: Cliff Reid on CG vs Illumina

http://mendeliandisorder.blogspot.com/2012/03/cliff-reid-on-cg-vs-illumina.html

Genomics . bioinformatics . biotechnology . sequencing . opinions. Monday, March 12, 2012. Cliff Reid on CG vs Illumina. Recently saw a post on the Complete Genomics website from Cliff Reid. Discussing our Nature Biotech paper (Lam et al, Dec 2011). In which we compared sequencing the same individual to high depth on both Complete Genomics and Illumina and compared them. This is certainly pretty cut-and-dried—obviously the CG-specific variants that we were able to validate. I think we need to consider a ...