Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • arne.muller
    Junior Member
    • Jun 2009
    • 3

    #31
    Hello,

    you mean exporting the current view into a graphics (e.g. png) file? I've had some relatively long response times during the export, but not as long as you report. I can imagine that the time needed for export is proportional to the number of elements in the current view. Maybe just take a screen shot for instead (not nice but often that's enough)?

    Arne

    Comment

    • The_Roads
      Member
      • May 2009
      • 38

      #32
      No sorry I meant turning on alignment info like coverage maps, non-specific reads etc. it takes a very long time for CLC to generate the graph in the top frame. likewise once the graph is there it takes ages to export a csv file of the graph. i'd like to know if anyone else has this problem or whether it might be something funky with my workstation (win6x 1x quad xeon 32Gb)

      Thanks

      Comment

      • smprince18
        Junior Member
        • Jun 2008
        • 4

        #33
        disclaimer I work at CLC bio

        The_Roads

        I was wondering if you have tried to contact [email protected] yet? Or you can reach us at (617)-444-8765. It could be a result that your VMoptions where not adjust correctly by the installer. If you go to the directory for the CLCGenomicsWB3 and show hidden, then you will see the .vmoption file, open this in notepad, there will be a line that looks like the following -Xmx####, where # = the number of mb allocated to the application (an example Xmx1024, means you have 1 gb of RAM allocated to the application)

        The second possibility you downloaded the 32 bit version of the application and not the 64 bit, this would result in very slow response time since, a 32 bit application can only request 2gb of ram)

        Again if you would like some help with this contact our support team or myself directly.

        Shawn M Prince

        Comment

        • The_Roads
          Member
          • May 2009
          • 38

          #34
          Hi Shawn,

          Thanks I'll be in touch.

          We have the 64 bit version and we've already tweaked vmoptions. Everything to relating to assembling, SNP detection etc. that requires 64 bit computing is working fine. It is just anything that alters the GUI or exports graphics/text that locks the workstations on large assemblies.

          The_Roads

          Comment

          • polsum
            Member
            • May 2009
            • 32

            #35
            Hi, I have been testing the trial version of CLC workbench and I encountered two issues.

            1. I BLASTed a set of illumina generated short reads (17-33, after trimming the 3'adapters) to mouse RefSeq database through stand alone BLAST program with stringent parameters and I found, say 2500 reads matching to mouse mRNAs. When I aligned all those 2500 reads to the same RefSeq database by using CLC reference assembly, only half of them are aligning to the reference. I tried all different options available changing the gap penalties, global alignment, scores etc...but never all the reads aligned to the reference. I think there should be more options here.

            2. I used BLAST feature in CLC bench and when I view the blast output parsed results, I dont see all the columns in the overview table. For example I dont see strand orientation titled column in the overview. However, I see it in the individual blast mapping, but it is useless for me because I need to count the total number of minus and plus mappings of the total number of mappings. This is a serious limitation for me.

            Comment

            • The_Roads
              Member
              • May 2009
              • 38

              #36
              As an update for future readers, received some excellent help from CLC and it appears the delays we experienced were due to the way we assembled our contigs. Using conventional assembly parameters graphics now render in seconds to minutes (CLC3.6.5).

              Comment

              • smprince18
                Junior Member
                • Jun 2008
                • 4

                #37
                Disclaimer I work for CLC bio

                Polsum,

                Once you Blast your sequences within CLC WB, you will be shown a graphic view of the results. If you look in the lower left hand corner of the working are you will see a table view. Once this is open you will see a default group of columns, Please note in the right hand side panel you can toggle on and off the columns you want to see.. You will be able to look at the direction of the results. Also if you are using this to reference map your reads we graphically show orientation (red = reverse read, green forward) Also the count of forward and reverse reads can be found in the contig report. Please let me know if this straightens anything up for you. If you would like I can be contacted at the CLC Boston office 617-444-8765.

                Shawn

                Disclaimer I work for CLC bio

                Comment

                • smprince18
                  Junior Member
                  • Jun 2008
                  • 4

                  #38
                  The Roads,

                  Glad to hear that your are enjoying your experience with CLC Genomics WB. Let me know if you need anything.

                  Shawn M Prince

                  Disclaimer I work at CLC bio

                  Comment

                  • johnny
                    Member
                    • Dec 2009
                    • 15

                    #39
                    Hey there,

                    one more newbie here
                    I have a probably easy to answer question but can't find the solution on my own....
                    How can I see the corresponding protein sequence to a nucleotide sequence ? In more detail, after a reference assembly, I would like to click through the variations with the "Find Conflict" button and instantly see if the protein sequence is affected as well.

                    Thanks for your help!

                    Comment

                    • The_Roads
                      Member
                      • May 2009
                      • 38

                      #40
                      Hi Johnny, I assume you are using CLCGWB. if so the conflict table is not the place to look. you should run a snp detection. if you have an annotated ref seq then the table will present you with all the amino acid changes.

                      Comment

                      • johnny
                        Member
                        • Dec 2009
                        • 15

                        #41
                        Yes, this is what I did before, but I also had numerous "conflicts" in the consensus sequence but no hit in the SNP detection. After changing the sensitivity I now found these variation as well. So thanks for bringing me onto the right track again.
                        What do you think is the minimum coverage to call a SNP ?

                        Comment

                        • The_Roads
                          Member
                          • May 2009
                          • 38

                          #42
                          Conflicts and SNPs are not really the same thing. In CLC a conflict is any variation from the ref seq or consensus. A SNP is a conflict that has passed quality and position requirements.
                          The minimum coverage for a SNP is debated a lot and obviously depends on your coverage and the type of project you are doing. For absolute reads, 8 reads that pass SNP calling is often used but i dont think there is really a gold standard, % all depends on your coverage. I would be very careful altering SNP quality or position criteria too much, you could easily end up with junk. CLC has excellent help on how SNPs are called. Vector and quality trimming and removal of broken reads should also improve the quality of your assembly before SNP detection. Gapped and ungapped assemblies can also give different SNP calls, particularly when there are conflicts between ref seqs and your consensus seqs. What type of project are you doing?

                          Comment

                          • smprince18
                            Junior Member
                            • Jun 2008
                            • 4

                            #43
                            ************************disclaimer I work for CLC bio ***********************

                            Johnny,
                            The Roads gave you a good answer to run the SNP detection, b/c you will have set significant values for the SNP. The conflict table will reflect anywhere you see a difference, you could have 100x coverage 99 a 1 c and that will be a conflict, but may not be included in the SNP table (depends on your sig values). The snp table will also reflect any AA change within annotated regions.
                            If however you would still like to use the conflict table you can go to the right hand side panel, go to the heading Nucleotide info and choose to show your translation, you can pick any and all frames or tell it to translate ORF and CDS regions. If you have more questions feel free to contact me (shawn prince) at [email protected]

                            Comment

                            • johnny
                              Member
                              • Dec 2009
                              • 15

                              #44
                              Originally posted by smprince18 View Post
                              If however you would still like to use the conflict table you can go to the right hand side panel, go to the heading Nucleotide info and choose to show your translation, you can pick any and all frames or tell it to translate ORF and CDS regions. If you have more questions feel free to contact me (shawn prince) at [email protected]
                              This is what I was actually looking for in the beginning. But I think there are more questions rising up while digging deeper into that subject. So I'll probaly take your offer and write an email instead of bothering the community .
                              Thank you both for the quick reply!

                              Comment

                              • didymos
                                Junior Member
                                • Jun 2010
                                • 8

                                #45
                                Hi,

                                I am wondering how big amount of RAM you need to assembly long contigs from human genome sequencing with short Illumina reads. On the CLC web page is writen that you need much less then in case of SOAP which was used in assembly of Panda genome. To get good coverage you need about 150-200Gb of reads (>50x coverage). In Panda genome project they used supercomputer with 512GB RAM....

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Pathogen Surveillance with Advanced Genomic Tools
                                  by seqadmin




                                  The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
                                  03-24-2025, 11:48 AM
                                • seqadmin
                                  New Genomics Tools and Methods Shared at AGBT 2025
                                  by seqadmin


                                  This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

                                  The Headliner
                                  The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
                                  03-03-2025, 01:39 PM
                                • seqadmin
                                  Investigating the Gut Microbiome Through Diet and Spatial Biology
                                  by seqadmin




                                  The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
                                  02-24-2025, 06:31 AM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 03-20-2025, 05:03 AM
                                0 responses
                                41 views
                                0 reactions
                                Last Post seqadmin  
                                Started by seqadmin, 03-19-2025, 07:27 AM
                                0 responses
                                46 views
                                0 reactions
                                Last Post seqadmin  
                                Started by seqadmin, 03-18-2025, 12:50 PM
                                0 responses
                                36 views
                                0 reactions
                                Last Post seqadmin  
                                Started by seqadmin, 03-03-2025, 01:15 PM
                                0 responses
                                191 views
                                0 reactions
                                Last Post seqadmin  
                                Working...