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How to cite the GTEx project

written 5 weeks ago by Bits of DNA by Lior Pachter

The GTEx consortium has just published a collection of papers in a special issue of Nature that together provide an unprecedented view of the human transcriptome across dozens of tissues. The work is based on a large-scale RNA-Seq experiment of postmortem tissue from hundreds of human donors, illustrated in Figure 1 of the overview by Ward […]

Feels like a dry winter – but what does the data say?

written 6 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

A reminder that when idle queries pop into your head, the answer can often be found using R + online data. And a brief excursion into accessing the Weather Underground. One interesting aspect of Australian life, even in coastal urban areas like Sydney, is that sometimes it just stops raining. For weeks or months at … Continue reading Feels like a dry winter – but what does the data say?

What we’re up to at ASHG 2017

written 6 weeks ago by Ensembl Blog

We’re really excited to be a part of the ASHG conference again, this time in Orlando from the 17th-21st October. We can’t wait to see all the great science that’s going to be presented, but here’s a guide to the talks, workshops and Continue reading What we’re up to at ASHG 2017→

What’s coming in Ensembl 91

written 6 weeks ago by Ensembl Blog

Ensembl 91 is scheduled for December 2017 and we’re continuing our push to include the genome annotation for lots of new species. This time, we’re adding a whole new set of primate species to Ensembl. Here’s what you can look forward to: Continue reading What’s coming in Ensembl 91→

PacBio's Frankenpatent on Error Correction

written 6 weeks ago by Omics! Omics! by Keith Robinson

Well, here we go again. Pacific Biosciences launched yet another patent lawsuit towards Oxford Nanopore at the end of September, and already the hounds are baying for me to look at the patents -- which I've foolishly established a reputation of doing. I will remind readers that, to use a construction that exasperates my son, I have no memory of these topics being covered during the time I was in law school. (said construction also works for divinity school, seminary, yeshiva, dental school, military academy, etc). Read more »

Dispatches from CDC AMD Day 2017

written 7 weeks ago by Omics! Omics! by Keith Robinson

I had the singular honor and pleasure of speaking this past Monday at the Center for Disease Control and Prevention's Advanced Molecular Detection(AMD) program's annual confab in Atlanta. Just visiting the CDC campus was already a bit magical -- along with the Kennedy Space Center and Cold Spring Harbor it's one of mythical places of human exploration to me. But to actually stand at the podium? Wow!I've collected below a bunch of separate mental threads, many of which probably should be expanded out to a full post in the future.Read more »

Use annovar to annotate variants

written 7 weeks ago by Diving into Genetics and Genomics

Annovar is one of the widely used variants annotation tools. It was cited for over 2000 times which is amazing. It annotates the variants in a tabular format which is easy to parse. Other tools such as VEP and VCFanno are alternatives.First download the annovar package (you will need to register and an email with downloading link will be sent to you)wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gztar xvzf annovar.latest.tar.gzDownload the databasescd annovarperl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/perl annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar snp129 humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03nontcga humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gnomad_genome humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar cadd13 humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar clinvar_20170130 humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar cosmic70 humandb/perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp33a humandb/AnnotateFirst download the annovar package (you will need to register and an email with downloading link will be sent to you) only 5 columns are needed for input: chr, start, end, ref, alt. By default, it assumes the file is in 1-based format.perl /scratch/genomic_med/apps/annovar/annovar/table_annovar.pl patient1_pre-treatment_vs_patient1_leukocyte_recount_alt_fill.txt /scratch/genomic_med/apps/annovar/annovar/humandb/ -buildver hg19 -out patient1_pre-treatment_vs_patient1_leukocyte_recount_annovar -remove -protocol refGene,cytoBand,snp129,cosmic70,dbnsfp33a,cadd13,clinvar_20170130,exac03nontcga,gnomad_genome -operation g,r,f,f,f,f,f,f,f -nastring NA -polish -otherinfo -thread 2perl /scratch/genomic_med/apps/annovar/annovar/table_annovar.pl patient1_pre-treatment_vs_patient1_leukocyte_recount_alt_fill.txt /scratch/genomic_med/apps/annovar/annovar/humandb/ -buildver hg19 -out patient1_pre-treatment_vs_patient1_leukocyte_recount_annovar -remove -protocol refGene,cytoBand,snp129 -operation g,r,f -nastring NA -polish -otherinfo

Upcoming API changes in Regulation for e!91

written 7 weeks ago by Ensembl Blog

The upcoming Ensembl release (e!91) will include several updates to the regulation API and with it a farewell to many objects that have given the regulation API its characteristic look and feel over the years. The changes listed below only Continue reading Upcoming API changes in Regulation for e!91→

Why Is LISP So Rare in Bioinformatics?

written 8 weeks ago by Omics! Omics! by Keith Robinson

LISP is one of the oldest computer languages and perhaps one of the most influential of the early ones. Some of the other well-known Eisenhower era languages -- Fortran, COBOL and ALGOL, have certainly left their mark, but LISP and derivatives such as Scheme or Common LISP certainly carries more cachet among "serious" programmers. COBOL has always been a bit of an easy joke and Fortran tends to mark you as old-school; use of APL (once a language of mine) would mark you as dangerously reactionary. ALGOL begat Pascal and Modula II and clearly had impact on the C syntax family of languages (including bioinformatics mainstays Python, Perl and Java) As I'll detail below, learning LISP has embarrassingly ended up stuck seemingly permanently on my future plans queue. But that's also because life never forced the issue: while LISP has certainly been used in bioinformatics (as covered in a review from 2016 ) , its mindshare in the community would seem to be very minimal.Read more »

Friday SNPpets

written 8 weeks ago by The OpenHelix Blog

This week we’ve got DNA in the gig economy and for sports fans (?), new software resources for virus and lipids, a handy collection of cancer genomics papers, microbiomes, biosecurity, sheep, pearl millet, and de-extinction. My favorite read this week, though, was the mosquito and gene drive review paper. I am so on board to gene-drive […]

Using the Open Science Framework to share files, for Science.

written 9 weeks ago by Living in an Ivory Basement by Titus Brown

Share files for fun and nonprofit.

Teaching Biology Evidence: Old or New?

written 9 weeks ago by Omics! Omics! by Keith Robinson

I've been toying over a week with writing something based on an interesting Twitter discussion started by Dr. Laura Williams (@MicroWavesSci) of Providence College pondering the best way to approach teaching molecular genetics (really, science in general) at the undergraduate level. In particular, Professor Williams wondered about the dangers of branding various key experiments with the names of the experimenters, such as Hershey-Chase or Meselson-Stahl. The risk she points out is that this can devolve into an exercise in memorizing names and dates without assimilating concepts, or conversely that some students will find the names more of a hindrance than a help. I'm going to play a bit with this, but I do emphasize that for her this is reality and for me it is a hobby (or perhaps a retirement fantasy, if I should ever actually retire). Or in other words, for the academic this is her industry but for this industrial scientist it is academic.Read more »

Classifying genome bins using a custom reference database, part II

written 9 weeks ago by Living in an Ivory Basement by Titus Brown

Classifying genome bins with a custom database! Part 2!

Friday SNPpets

written 9 weeks ago by The OpenHelix Blog

This week I left the “call to action” tweet at the top–you could vote for GenBank every day until the end of the competition. Today’s the last day. Vote once more. And remember how resources like GenBank let us have foundations for other important resources as well. There are new resources in this week’s SNPpets that are definitely […]

Ensembl Genomes 37 is now live

written 10 weeks ago by Ensembl Blog

We’re pleased to announce the latest release from Ensembl Genomes. There’s new data and software available. Find out more: Plants New genomes for Jute (Corchorus capsularis) and Cassava (Manihot esculenta). Updated genome assembly for Sorghum (Sorghum bicolor) New cross references Continue reading Ensembl Genomes 37 is now live→

Infographic-style charts using the R waffle package

written 10 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

Infographics. I’ve seen good examples. I’ve seen more bad examples. In general, I prefer a good chart to an infographic. That said, there’s a “genre” of infographic that I do think is useful, which I’ll call “if X were 100 Y”. A good example: if the world were 100 people. That method of showing proportions … Continue reading Infographic-style charts using the R waffle package

Friday SNPpets

written 10 weeks ago by The OpenHelix Blog

This week I left the “call to action” tweet at the top–you could vote for GenBank every day until the end of the competition. On other fronts, there’s big media on Venter’s DNA re-identification article–but there’s also significant blowback on that. A series of tweets in there gets to that. Otherwise, more of the other cool things in […]

Getting to know us: Sophie from the Research Management Office

written 10 weeks ago by Ensembl Blog

Our latest introduction to the Ensembl Team post comes from Sophie Janacek, who takes care of all our money. What is your job in Ensembl? I am a ‘Research Manager’: I help Ensembl to manage its grant and funding portfolio, and to Continue reading Getting to know us: Sophie from the Research Management Office→

Classifying genome bins using a custom reference database, part I (Saturday Morning Bioinformatics)

written 10 weeks ago by Living in an Ivory Basement by Titus Brown

Classifying genome bins! With pictures!

Taxonomic examinations of genome bins from Tara Oceans (Honorary Sunday Morning Bioinformatics)

written 11 weeks ago by Living in an Ivory Basement by Titus Brown

An initial taxonomical investigation of the genome bins.

A rebuttal

written 11 weeks ago by Bits of DNA by Lior Pachter

In a previous post I wrote about How not to perform a differential expression analysis. In response to my post, Rob Patro, Geet Duggal, Michael I Love, Rafael Irizarry and Carl Kingsford wrote a detailed response. Below is my point-by-point rebuttal to their response (the figures and results in this blog post can be generated […]

Comparing genome sets extracted from metagenomes (Sunday Morning Bioinformatics).

written 11 weeks ago by Living in an Ivory Basement by Titus Brown

Two different binning procedures, on different data, produce somewhat different bins. Duh.

Friday SNPpets

written 11 weeks ago by The OpenHelix Blog

This week I left the “call to action” tweet at the top–you can vote for GenBank every day in August. And I know it’s September now, but I wanted to go and check–and they made it to the final four! So go vote for GenBank some more. Same link works fine. Other things this week: NYTimes shows […]

Adjusting Custom Tracks in Ensembl

written 11 weeks ago by Ensembl Blog

In the latest Ensembl release (Ensembl 90, August 2017), we have added the option for you to adjust the y-axis of your custom “wiggle” tracks, such as BigWig and bedGraph files. You can now choose the track parameters when uploading a BigWig Continue reading Adjusting Custom Tracks in Ensembl→

Is your bioinformatics analysis package Big Data ready?

written 11 weeks ago by Living in an Ivory Basement by Titus Brown

Plan for incremental data updates when building your tools.
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