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Friday SNPpets

written 2 days ago by The OpenHelix Blog

This week included the first day of summer, and I lost the thread just a little bit. But there were some fun things. Tindr for preprints? Really? GWAS drama. Legal issues. Cats domesticating humans, or something. Ok, maybe that’s just my house. Welcome to our Friday feature link collection: SNPpets. During the week we come […]

Visualising Twitter coverage of recent bioinformatics conferences

written 5 days ago by What You're Doing Is Rather Desperate by Neil Saunders

Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the VIZBI 2017 meeting. So without further ado, here are the reports in markdown format, … Continue reading Visualising Twitter coverage of recent bioinformatics conferences

Ensembl Genomes 36 is now live

written 6 days ago by Ensembl Blog

We are pleased to announce that Ensembl Genomes 36 has now been released, which includes new and updated genome assemblies and gene annotation as well as updated variation data and comparative genomics analyses. Find out more below: Ensembl Bacteria includes an additional 142 Continue reading Ensembl Genomes 36 is now live→

Friday SNPpets

written 9 days ago by The OpenHelix Blog

This week was yummy. Apple epigenome and a new corn assembly, in time for your northern hemisphere summer picnics. Marine protists for you to think about during your walks on the beach. The return of the Venn, and a guide to PCA plots. A very cool set of human protein complexes. Synbio tools. My favorite this week, though, […]

What’s coming in Ensembl release 90

written 9 days ago by Ensembl Blog

Ensembl 90 is scheduled for July 2017 and it’s set to be our biggest release ever in terms of new genome annotation. Here’s what you can look forward to: New assemblies, gene sets and annotations Annotation of 15 rodent genomes, including three updates Continue reading What’s coming in Ensembl release 90→

New Life in the Sanger Market

written 10 days ago by Omics! Omics! by Keith Robinson

In my bit on "I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases. Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard. Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small labs, and according to GenomeWeb Promega plans an instrument offering in the same space as well.Read more »

bwa aln or bwa mem for short reads (36bp)

written 10 days ago by Diving into Genetics and Genomics

My ChIP-seq data are 36bp single end reads. I usually use bowtie1 for mapping ChIP-seq reads, but bowtie1 does not handle indels. Since I want to call mutations on the ChIP-seq reads, I have to use another aligner BWA, the most popular mapper written by Heng Li.The github page says if reads &lt; 70bp, bwa aln should be used. Otherwise, bwa mem should be used.bwa mem is a more recent algorithm (should be better?).I searched on biostar, and found When and why is bwa aln better then bwa mem?I did a simulation test using Teaser using default setting for each aligner.The results are shown below:The mapping rate:Memory usage:Run time:Indeed, BWA aln is a little better than BWA mem for short reads.For a real data set, the samtools flagstat results are shown below:bwa aln:282967631 + 0 in total (QC-passed reads + QC-failed reads)0 + 0 secondary0 + 0 supplementary18963259 + 0 duplicates240660130 + 0 mapped (85.05% : N/A)0 + 0 paired in sequencing0 + 0 read10 + 0 read20 + 0 properly paired (N/A : N/A)0 + 0 with itself and mate mapped0 + 0 singletons (N/A : N/A)0 + 0 with mate mapped to a different chr0 + 0 with mate mapped to a different chr (mapQ&gt;=5)bwa mem:282967631 + 0 in total (QC-passed reads + QC-failed reads)0 + 0 secondary0 + 0 supplementary18332921 + 0 duplicates236558306 + 0 mapped (83.60% : N/A)0 + 0 paired in sequencing0 + 0 read10 + 0 read20 + 0 properly paired (N/A : N/A)0 ...

Getting to know us: Matthew from Core

written 16 days ago by Ensembl Blog

This is the third of our monthly posts introducing a member of the Ensembl team and what they do in Ensembl. This time it’s Matthew Laird, who works in the Core team. What is your job in Ensembl? I’m a Continue reading Getting to know us: Matthew from Core→

A tweak to Ensembl transcript IDs

written 17 days ago by Ensembl Blog

Ensembl transcripts have two identifiers, the versioned ENST, which is stable through time and can be tracked from release to release, and a separate identifier that incorporates a gene symbol. The latter have changed in e!89; read on for more Continue reading A tweak to Ensembl transcript IDs→

Ice Ghosts:A Shortage of Maps

written 18 days ago by Omics! Omics! by Keith Robinson

I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics). Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage. It's a pretty good book, after all it did win a Pulitzer Prize, The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century. There are lessons for science in general, such as the value in carefully evaluating oral histories that some would discard as unreliable. But what is maddening for me is that in a book for which a central theme is poorly understood geographies and their interpretations, the set of supplied maps fail miserably at assisting in the telling of the story.Read more »

Weather and crimes in Chicago

written 19 days ago by Diving into Genetics and Genomics

Weather and crimes in ChicagoMing TangJune 4, 2017How the story startsI was attending 2017 American Society of Clinical Oncology (ASCO) annual meeting in Chicago. It was my first time to do a uber from the airport to our hotel. We had a nice uber driver and we talked a lot about the city. He said he grew up in the south part of Chicago and there are a lot of crimes there. He knows the city so well that he tries his best to avoid bad districts to pick up customers. When strangers meet, topic will always be weather. I certainly joked about the badness of winter in Chicago and he replied back with the badness of hotness in Houston.He said there are around 600 cases of shooting per year in Chicago, and in the holidays such as Memorial day, shooting arises to 40 per day. I asked him why do you think there is such an increase. He said: I think it has to do with the weather. In the Memorial day, it becomes warmer. everybody has access to everybody. that’s why the crime rate is higher as well."As a budding data scientist (that’s how I define myself) to interrogate data from DNA sequencing on tumor samples, I should not just take his words, I want to verify this by some evidences. Initially, I was surprised that weather can be associated with crime rate. Then I googled around when I got the hotel and it turns out that this ...

Friday SNPpets

written 23 days ago by The OpenHelix Blog

This week was big on #CRISPR stuff. That drama about the off-target alterations, and the pushback, consumed much oxygen. But there’s plenty of the usual stuff too–new software, personalized medicine marches on, DTC genetic testing issues, new samples from ancient sources. Best thing: the script to convert fastq to emojis. Oh–I’m off next week because I’ll […]

Ensembl 89 has been released!

written 25 days ago by Ensembl Blog

Ensembl 89 is now live. Read on to find out about the new features and data in this release. Updated assemblies, gene sets and annotations: Human: updated cDNA alignments Mouse: updated cDNA alignments and update to Ensembl-Havana GENCODE gene set Other: Variation Continue reading Ensembl 89 has been released!→

RNA-Seq for Mendelian Disease Cases

written 4 weeks ago by MassGenomics by Dan Koboldt

Next-generation sequencing technologies have transformed the way we study rare genetic disorders. Exome sequencing for Mendelian disease is the poster child for success in this arena. However, despite the frenzied pace of disease gene discovery and the growth of public sequence databases, the diagnostic/success rates for exome sequencing have remained somewhat constant over the past several years. […]

Friday SNPpets

written 4 weeks ago by The OpenHelix Blog

This week includes one of those stories that reminds me of the power of databases. See that diagnostic odyssey of a family with a child with mystery symptoms and the doctor who sleuthed out some information–then connected with other families awaiting answers (Hudson Alpha tweet). But then there’s also the looming issues of misuse of […]

Judge rules in favour of Oxford Nanopore in patent dispute with PacBio

written 4 weeks ago by Opinionomics by Mick Watson

Forgive me if I get any of the details wrong, I am not a lawyer, but the title of this post is my take on a judgement passed down in the patent infringement case PacBio brought against ONT. To get your hands on the documentation, you need to register and log in to EDIS, click […]

Video Tip of the Week: Direct to Consumer Genetic Testing and Genetic Counselling

written 4 weeks ago by The OpenHelix Blog

At OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, I know, it still varies). But outreach really is getting better. There are journals now that are also enforcing more reader-friendly ways to describe the research, with non-jargon summaries and some terrific visual […]

Find us at PAG Asia in Seoul

written 4 weeks ago by Ensembl Blog

Ensembl will be at two conferences in late May: ESHG in Copenhagen and PAG Asia in Seoul. If you’re at PAG Asia, we hope to see you at our workshop and the poster sessions! Genomic Annotation Resources at the EBI: Continue reading Find us at PAG Asia in Seoul→

What Is (and Is Not) Sequence Assembly?

written 4 weeks ago by Omics! Omics! by Keith Robinson

In the closing talk of the pre-London Calling workshop, Hans Jansen had closed his presentation with a question whether at some future date sequence assembly would become obsolete. This was meant to be an aspirational vision for a distance timepoint, but one correspondent on Twitter saw it as hype. I got in a bit of a discussion, constrained by the dreaded 140 character limit, which ended up largely illustrating that I have a somewhat more restricted definition of assembly than some people. I'm going to explore this and you can judge for yourselfRead more »

when NAs are not NAs

written 4 weeks ago by Diving into Genetics and Genomics

Downloading dataUsing TCGAbiolinks, I downloaded RNAseq data for LUAD and LUSClibrary(TCGAbiolinks)library(SummarizedExperiment)# query_rna_LUAD.hg38 &lt;- GDCquery(project = "TCGA-LUAD", data.category = "Transcriptome Profiling",# data.type = "Gene Expression Quantification", # workflow.type = "HTSeq - Counts")# # # query_rna_LUSC.hg38 &lt;- GDCquery(project = "TCGA-LUSC", data.category = "Transcriptome Profiling",# data.type = "Gene Expression Quantification", # workflow.type = "HTSeq - Counts")# # GDCdownload(query_rna_LUAD.hg38, method = "client")# GDCdownload(query_rna_LUSC.hg38, method = "client")# # LUAD_rna_data &lt;- GDCprepare(query_rna_LUAD.hg38)# LUSC_rna_data &lt;- GDCprepare(query_rna_LUSC.hg38)# I have saved both R objects into diskload("~/projects/mix_histology/data/TCGA_rna/TCGA_lung_rna.rda")# a RangedSummarizedExperiment objectLUSC_rna_data## class: RangedSummarizedExperiment ## dim: 57035 551 ## metadata(0):## assays(1): HTSeq - Counts## rownames(57035): ENSG00000000003 ENSG00000000005 ...## ENSG00000281912 ENSG00000281920## rowData names(3): ensembl_gene_id external_gene_name## original_ensembl_gene_id## colnames(551): TCGA-77-8009-01A-11R-2187-07## TCGA-34-5239-01A-21R-1820-07 ... TCGA-NK-A7XE-01A-12R-A405-07## TCGA-43-6773-11A-01R-1949-07## colData names(69): patient barcode ...## subtype_Homozygous.Deletions subtype_Expression.SubtypeThe problem is with the meta dataLUSC_coldata&lt;- colData(LUSC_rna_data)LUAD_coldata&lt;- colData(LUAD_rna_data)we will see the different representations of NAstable(LUAD_coldata$subtype_Smoking.Status, useNA = "ifany")## ## Current reformed smoker for &gt; 15 years ## 78 ## Current reformed smoker for &lt; or = 15 years ## 77 ## Current smoker ## 47 ## Lifelong Non-smoker ## 32 ## [Not Available] ## 11 ## &lt;NA&gt; ## 349table(LUSC_coldata$subtype_Smoking.Status, useNA = "ifany")## ## Current reformed smoker for &gt; 15 years ## 51 ## Current reformed smoker for &lt; or = 15 years ## 87 ## Current smoker ## 28 ## Lifelong Non-smoker ## 7 ## N/A ## 6 ## &lt;NA&gt; ## 372we see NAs are represented either as real &lt;NA&gt;, [Not Avaiable] or N/A. The first thing to do is to tidy the metadata changing all NAs to &lt;NA&gt;:I will use stringr from the ...

Developing R package: library specific functions

written 5 weeks ago by thoughts about ...

Recently started developing an R package with focus on Bioconductor. Had a lot of experience in using R, but package development in this language is a novel area for me. Got into very strange problem: testing code of function out of package works well, but activating this function from prebuilt package leads to error. The problem was with usage of "intersect" base operation. By default it was loaded from sets library, while was required from GRanges in my case.Spend some time to figure this out, but thanks to this post fixed it. Issue was related to additional marking of function origin in DESCRIPTION. Basically, additional mark was required in Roxygen function annotation:#' @importMethodsFrom GenomicRanges intersectAlso, one thing that I had to control - frequent reload of library to run testing. The following command works well:detach("package:InTAD", unload = TRUE)Of course, easier testing can be organized using testthat, but initial coding requires simple reload. These are only minor issues, but closer to Bioconductor submission attempt I will try to give more overview.

Friday SNPpets

written 5 weeks ago by The OpenHelix Blog

This week, quite a range. From crops in silico, to antique tumor samples to assess cancer genomes. Even older: assessing ancentral variants to battle todays viruses. That’s right–we are standing on the past and in the future. Deadly tropical snails. At NCBI–the end of BLink. And other useful things. Welcome to our Friday feature link collection: […]

What we’re up to at ESHG 2017

written 5 weeks ago by Ensembl Blog

We’re really excited to be a part of the ESHG conference again, this time in Copenhagen from the 27th-30th May. 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 Continue reading What we’re up to at ESHG 2017→

London Calling 2017: Plant &amp; Animal de novo Genomes

written 5 weeks ago by Omics! Omics! by Keith Robinson

Okay, I'm desperately behind on writing up the external science from London Calling. Not helpful that I claimed I would not only do so, but in multiple installments. A number of the plenaries focused on large genome assembly, so that's what I'll tackle now -- plus a few other bits. See also my Storify summaries, which include other reports on the conference. Also check out my storifies on the SMRT Leiden conference, which ran at the beginning of the same week and discusses many similar topics.Read more »

Video Tip of the Week: On The Turing Completeness of PowerPoint

written 5 weeks ago by The OpenHelix Blog

This week’s video tip is…well…atypical. It’s not about a software tool, per se. Or, is it…?
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