Tag Archives: NGS

SNPpets_2

Friday SNPpets

This week’s SNPpets have a range of resources–from food crops to public health to personal genomics. Really, it’s touching everything we do now. A resource filling a gap–digenic diseases–was new to me: DIDA.  A nice collection of miRNA resources. And a popular item about NGS can go “horribly wrong”. An awesome FAQ. The final JABBA award. There’s a lot more too–great week for fascinating reads.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


https://twitter.com/ACGT_blog/status/696816305945632768

Video Tip of the Week: DNA Subway

At a recent training workshop on the UCSC Genome Browser, I spoke with an educator who is using a custom local installation of the browser to work with students on bioinformatics lessons. It’s a project called the Genomics Education Partnership at WashU, and students learn by annotating regions of the genome with bioinformatics tools. You can see the team’s installation of the browser here. It sounded like an enjoyable and effective method and useful to students.

So the other day when I was exploring some of the resources available from the iPlant Collaborative, I was reminded of the annotation educational method by their very cool DNA Subway project. It’s another strategy to educate students with genome annotation tools–but I also think there might be some scientists who might want to use it beyond formal educational settings. It’s not new–I can remember reading about it in the past, but looking at it again with fresh eyes after that other conversation was worthwhile. And they’ve added new features since I last explored.

Student annotation projects are widespread, and there are probably numerous different successful strategies that local folks have implemented to set this up. But I suspect that more folks who are teaching bioinformatics might find the workflow infrastructure of the DNA Subway system a useful mechanism to use themselves, rather than setting up their own. So this week’s video tip of the week highlights the DNA Subway. Oh–and by the way: just because it’s at iPlant doesn’t mean it’s restricted to plants. You can go over there and see the various species options.

The providers of the Subway describe it as:

DNA Subway makes high-level genome analysis broadly available to students and educators and provides easy access to the types of data and informatics tools that drive modern biology. Using the intuitive metaphor of a subway map, DNA Subway organizes research-grade bioinformatics analysis tools into logical workflows and presents them in an appealing interface.”

I thought this was a really effective way to conceptualize the tasks that need to occur on a project. And it’s integrated with the tools you need at each “stop” to accomplish the tasks. The new “green line” in Beta that they have created isn’t shown in the video, but you should have a look at the site. It’s got tools for NGS RNA-seq data analysis, integrating the Tuxedo workflow protocol that includes TopHat, Bowtie, and Cufflinks, and is a really good thing for students to be exposed to. If you go over to the DNA Subway site itself and choose the “green line” to explore, you can see more information.

I can’t seem to embed their video, so I’d recommend you look at the larger size version on a separate page, and to go over and have a look for yourself at the DNA Subway.

Go over to their site by clicking on the image to access the video.

Go over to their site by clicking on the image to access the video.

Quick links:

DNA Subway main description page: http://www.iplantcollaborative.org/discover/dna-subway

DNA Subway installation: http://dnasubway.iplantcollaborative.org/

DNA Subway video tour (larger size): http://dnasubway.iplantcollaborative.org/files/tour/index.html

References:

Goff S.A., Vaughn M., McKay S., Lyons E., Stapleton A.E., Gessler D., Matasci N., Wang L., Hanlon M. & Lenards A. & (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology, Frontiers in Plant Science, 2 34. DOI:

Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., Pimentel H., Salzberg S.L., Rinn J.L. & Pachter L. & (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (3) 562-578. DOI:

What’s the Answer? (Next-Generation Sequencing -NGS- courses)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question was created 18 months ago, but new slides and comments have been added and is still an excellent resource for a course on NGS:

Question: I am preparing a course on NGS: any suggestion ?

The first answer (with 22 up votes!) is a treasure trove of material, along with some excellent resources from other answers. Want to learn more about analysis of NGS data?… here you go.

Must see: Richard Resnick TEDxBoston talk

Recently my twitter feed was burning up at the live presentation at TEDxBoston by Richard Resnick. I had caught most of it (thanks to the tweeps who sent word), and scribbled down a few notes. But mostly I wrote in my notebook that I needed to seek out this talk on the web later and review it. Just found it–and you need to watch it.

Richard Resnick gives an excellent presentation of the state of genome sequencing today–the rate and the increase–with just a couple of minutes and some well-done graphics. But he quickly moves to what this means for medicine today.

He describes a typical case of a woman’s cancer and the medical interventions for it over the last few years–and says that this will look like bloodletting to us in the near future because it’s so primitive. He explains how her genome and that of her cancer was examined to discover issues.

He relates the story of the twins who were discovered to have a treatable condition based on their genome sequencing, after suffering for years with unknown problems. And the story of Nick, who Matthew Herper called The First Child Saved By DNA Sequencing.

“The prospect of using the genome as a universal diagnostic is upon us today.”

He talks about how this can give all of us extra years of health. But he also turns to how this impacts the planet, including food production which is being affected by this technology too–and says:

Now look, as long as we continue to increase the population, we’re going to have to continue to grow and eat genetically modified foods. And that’s the only position I’ll take today.

Next he places the genomic revolution into personal context and consumer uses and social implications. He shows an application he had for life insurance which *specifically* demands to know if you have had a personal genomics test done. (By the way, the US GINA legislation does not prevent discrimination based on your genome for this kind of insurance–a lot of people don’t realize that).

The excitement of the time we live in, with appropriate warnings about the implications, are really well done in this talk. And he asks everyone watching to wake up and influence the genomic revolution we are in.

It’s just over 11 minutes long. Watch it. Srsly. Worth your time.

In case the embed doesn’t work, or to watch embiggened, go here: http://tedxtalks.ted.com/video/TEDxBoston-Richard-Resnick-Th-2

TEDxBoston – Richard Resnick – The Next Hot Commodity of Genome Sequences

What’s the Answer: Open Thread (NGS Tools)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the
community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the week:

Now we are analysing NGS data, and I wonder if you know some collections of bioinformatics tools which can help me (like biopieces).

There were a few good answers with a good suggestion of lists of tools for analysis and preparation of Next-Generation Sequencing tools. Here’s one answer, click the link above for the rest:

(after some advice about mastering scripting language and unix commands…)

  1. learn the most used bioinformatics tools. e.g.:
    • one (or preferably many) short-read aligners
    • samtools
    • an NGS viewer (IGV is a good one to start)
    • Bedtools
    • A means to view and filter your NGS reads
    • and certainly many others depending on your specific focus.
  2. Then start to learn some of the common data repositories. e.g.:

 

“What’s the Answer?” Thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:
With the advent of NGS data, lots of people have been looking for ways to visualize the BAM and SAM files for further analysis. We’ve been coming across that a lot in our workshops lately. I think you might be able to do that pretty well with a custom track at UCSC Genome Browser, though it’s probably not as simple as some tools listed and sometimes you need more. Today’s biostar question and answer:

…I want to know is there any freely available software for the visualization of the aligned reads including their sequences for Bowtie output (sam or bam format)….

Highlighted Answer:
The most up-voted answer was a simple one sentence:

See this great blog post reviewing several NGS genome viewers (they all read BAM format).

(It is a great blog post). There are other answers too that were helpful, check out the discussion…

Have some NGS SAM/BAM files? get a GUI interface

A recent paper on a GUI interface introduces SAMMate. As the paper states:

With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files.

You might want to check it out if you have Next Generation Sequencing data in the form of BAM/SAM files. A nice feature I haven’t been able to check is that it will export a ‘wiggle’ file for alignment visualization in the UCSC Genome Browser.

Next-Generation Analysis Tools

MassGenomics points to a new structured programming framework for analyzing NGS data: A Foundation for Next-Generation Analysis Tools, the GATK (Genome Analysis Toolkit) and points to a few tools that use it.

While I’m at it, let me remind you of a NGS discussion group, GBrowse help to visualize NGS data and Galaxy has a NGS toolbox.