Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Genomatix
    replied
    Actually, it is possible, and we do it, but this is not the right thread for that kind of post. I will put something out on the vendor forum shortly. Have a look.

    Leave a comment:


  • joa_ds
    replied
    well, in my opinion you cannot develop a commercial package for next-gen sequencing that is so versatile that you can use it as THE analysis tool for your sequencer.

    I agree you can make a system that stores and annotates, even maps, your sequences. But automating your complete analysis or conclusion is almost impossible.

    What if you do a transcript counting run in january, a bisulfite run in february, SNP discovery run in march and a de novo run in april? I hardly doubt that a commercial package can do all this work.

    So you will need to work modular and automate the modular selection of certain packages. We are working on that here. Trying to think outside the box and always thinking 'can this part of the pipeline be used in other types of experiments'. This is the kind of things I missed in the conference.

    The grapevine virus was quite interesting, because it was one of the few examples that showed that a specific question combined with a sequencer can generate interesting results that are immediately usable. I have a bit the feeling that the we are evolving to a situation where genomes are sequenced and people are trying to figure out what to do with the sequenced genomes.

    The other examples were also interesting, but they explained the front prep, the sequencer and then skipped to the results and in the end they say 'data analysis is a very hard task'. I know cancer is a major research field, i know transcript counting is a major research field, but everyone knows that, no? but how to get those results?

    And all the fancy companies offering fancy data storage is ok for me. I can imagine a Venter institute or Broad institute or CompleteGenomics can use that, but when I see that a new grapevine virus can be discovered using only spreadsheets, i was quite amazed. I would have liked to see more of those analysis pipelines.

    My guess is that:
    a) people are letting specialised groups do the data analysis?
    b) the analysis pipelines are secret?
    c) analysis is still underway?

    I was quite surprised because whenever you read a sequencing paper, the analysis pipeline is always mentioned in a nice figure and they always mention some basic metrics such as %mapped, %unmapped, %mixed, avg length...

    I don't know, might be me, this was my first conference ever. No idea what is like on other conferences

    Leave a comment:


  • Genomatix
    replied
    Pardon if this is a repeat. Please visit the vendor forum There are "analysis solutions" available, but agree they were not well represented at the conference. Much talk about the front end (sample prep) etc. Lots of talk about the numbers...very little talk about the analysis and the BIOLOGY that the experiment was done for in the first place.

    That's what we are all about...

    Leave a comment:


  • Genomatix
    replied
    Please visit the vendor forum. There are "analysis solutions", but agree they were not well represented at the conference. No commercial announcement here...

    Leave a comment:


  • swbarnes2
    replied
    Originally posted by joa_ds View Post
    I can belief you store a single 454 run in an excel sheet, but what then? No one is using DB systems that were created in houes? No one has build custom pipelines?
    I remember that talk. Those grapevine virus people got suckered by GenomeQuest. They could have done most almost everything they wanted to in Access. Because Access is a database program, and Excel isn't. They could have gotten a MySQL database too, but Access is nice and safe and familiar, and they almost certainly already had the license. But they didn't even understand the difference between a spreadsheet and a database.

    Leave a comment:


  • joa_ds
    replied
    well, this was my first conference ever as i only started my PhD some months ago. Being transatlantic alone in the Hilton, well it aint that bad, but it is kind of 'woooowing'.

    I thought it was very interesting to see what is coming in the next-next gen field. Kinda disapointing as well, makes you feel small. We had the biggest academic cluster installed of Western Europe (6000 cores) and then you see Complete genomics announcing a plan for a 60k cluster with 15 PB storage !!! We are back to eating the crumbs of the bread.

    I was only a bit disapointed with the data management and data analysis part of the conference. There was a talk on Gene Wiki, which is nice to see, but i could have made that also. For the rest there was some commercial talks on data storage systems and file systems, but no real data analysis explanation. I can belief you store a single 454 run in an excel sheet, but what then? No one is using DB systems that were created in houes? No one has build custom pipelines?

    We all know sample prep and downstream processing are the hardest part. The sample prep was widely discussed on the conference, the sequencing itself also, but what then? And then i saw a lot of nice figures and results. But between the sequencing and the figures there is a big dark hole for me. I don't belief that anyone is actually using AVA software for a titanium run? or is manually blatting all the 454 sequences... Would have been nice to see some pipeline or custom solutions.

    Maybe the organizers felt the same? and are therefore planning to split the sequencing in rhode island in 'sequencing and 'data analysis', which makes it very tempting to go again in another 6 months...

    Leave a comment:


  • Genomatix
    replied
    CHI is a bit overwhelming, but thought the event well run and with some very high quality presentations, albeit some were "commercial" in nature. Since I come from that side, I'm probably a bit prejudiced, but thought even the vendor presentations good without too much flag waving. Some great science as well, including several presentations on the "next-next" generation of machines. FWIW...

    Leave a comment:


  • doxologist
    replied
    Originally posted by 2007lab View Post
    Would there be some kind of Video Archive for us to peek into after the conference is over? like AACR for e.g.?
    They sell DVDs of their recordings... I believe it's a very high price. (correct me if I'm wrong)

    Leave a comment:


  • strob
    replied
    Can you give us a status regarding the Helicos package?

    Leave a comment:


  • vruotti
    replied
    Conference update.

    Interesting Panel discussion today.
    A representative from Illumina, Roche, Solid and Helicos were all side by side answering questions from the audience.

    The common problem was scalability. All four are working on trying to use a little sample as possible (well as Helicos) and make easier to run more samples. Gel/PCR free protocols are on the way.
    Have not heard of a GAIII yet from Illumina. I did hear from the 1.4 pipeline.
    It supposed to do a better job extracting intensities from images. So, do we save the images after all?

    victor

    Leave a comment:


  • vruotti
    replied
    If there is enough interest... How about getting together tomorrow Wed. There is a question-answer session at 5:40. Maybe after this session?

    If this doesn't work perhaps Thursday during lunch?
    Victor

    Leave a comment:


  • mchaisso
    replied
    My guess is no, but I'll post my slides online (still trying to cram one or two in though now).

    Leave a comment:


  • 2007lab
    replied
    Would there be some kind of Video Archive for us to peek into after the conference is over? like AACR for e.g.?

    Leave a comment:


  • mchaisso
    replied
    I'll be there and am interested in hearing of short read aligning headaches, but I'll only be around intermittently since this is a very busy month for me. I'll follow this thread to find out where to meet.

    Leave a comment:


  • vruotti
    replied
    Small Group Gathering regarding aligners

    Hello,
    I will be attending the CHI conf in San Diego and for the ones that are interested in aligners I would like to propose a small group discussion in between talks.
    Date and time will be determined soon. Will anyone be interested on getting together to share ideas re the storm of aligners and the short read headache we all tend to deal with?

    Victor

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
197 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
206 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
190 views
0 likes
Last Post seqadmin  
Working...
X