Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    Originally posted by strob View Post
    Again, I had no trouble getting the software. They just asked me where we get our sequences from (which provider), and a few days later the DVD's were in my mailbox....
    Perhaps different policy for latin america?
    I received the answer from:

    Head
    Roche Applied Science
    Roche Diagnostics Chile

    However he asked me to write a letter to justify why I need the software and for what. I find this quite annoying since I can't imagine another use but to assemble DNA sequences. Anyway...

    ---sram
    Last edited by sram; 09-11-2009, 05:08 AM.

    Comment


    • #17
      Originally posted by strob View Post
      I work indeed in Belgium, Europe. And I even work in a commercial company....

      At the PAG meeting I discussed this with Roche at their booth and they just told me that I should contact my local contact. After 1 phone cal, I received the software.
      OK. So I don't understand my experience with Roche here in Chile.
      Thank you for your message.
      Regards,

      ---sram

      Comment


      • #18
        Hey
        the same here for me (in the Netherlands). I didn't even ask for the software but since our University already had an older (GLX) one and now have a Titanium..... They just asked whether the software might be useful to have.... of course ... next day the DVDs and 3 days later the thick manual in print on my desk
        For large assemblies I think you need quite a strong linux computer though...
        Alex

        Comment


        • #19
          Another positive example: we asked about this via our local sequencing centre (in the UK), and Roche was happy for them to make Newbler available to us and other users.

          Did you have any progress with Roche's Chile representatives srcam?

          Comment


          • #20
            Newbler DvD's

            Hi there,

            I had the same problem here in Argentina, I was wondering if maybe someone could ship me a copy of the Newbler DVD's. I would of course pay for the shipping costs and the copy.
            If possible, please send me an email.

            Thank you very much

            Comment


            • #21
              Hi there,

              I 've requested Roche a software copy from their support page, hope they consider sending me the DVD's to Argentina.

              Having this in mind I wanted to ask in the forum wich alternative would you recommend me for de novo genome assembly using roche's 454 .sff files.

              Celera, CLC, Velvet, GenomeQuest, Arachne, etc?

              Issue#2: Any ideas from where I could get a pipeline procedure for cleaning (trimming) the 454 files in order to prepare the seqs for assembly.

              Thank you very much for any information,

              Wish you all a Merry Xmas and a Happy new year

              Best Regards,

              Gabriel

              P.S: It's a Plant Genome.

              Comment


              • #22
                Hi Gabriel,

                Originally posted by gabriel.lichtenstein View Post
                Hi there,

                I 've requested Roche a software copy from their support page, hope they consider sending me the DVD's to Argentina.

                Having this in mind I wanted to ask in the forum wich alternative would you recommend me for de novo genome assembly using roche's 454 .sff files.

                Celera, CLC, Velvet, GenomeQuest, Arachne, etc?
                Depends on what you are expecting and if you are willing to spend (a lot) of money for software ...

                Celera works fine if you have PE libraries, final result can be converted to ace which can be edited with consed. We are working on a CAF converter as well. CLC may work fine as well, cost a lot of money, ace export is poor. I'd only use velvet for short reads, not for 454 and/or sanger data, but that is my personal opinion ;-)
                You might also want to have a look at MIRA3 (http://chevreux.org/projects_mira.html).


                Issue#2: Any ideas from where I could get a pipeline procedure for cleaning (trimming) the 454 files in order to prepare the seqs for assembly.
                What do you want to trim? The quality trimming is usually done by the roche software itself. If you have a genomic library there should not be too much to clip off ...

                cheers from lima/peru (just for vacation, sigh),
                Sven

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Current Approaches to Protein Sequencing
                  by seqadmin


                  Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                  04-04-2024, 04:25 PM
                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 04-11-2024, 12:08 PM
                0 responses
                31 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 10:19 PM
                0 responses
                33 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 09:21 AM
                0 responses
                28 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-04-2024, 09:00 AM
                0 responses
                53 views
                0 likes
                Last Post seqadmin  
                Working...
                X