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  • #31
    In my point of view there are goods changes and i am happy to learn about this new version.
    But, why doesn't illumina make aware its users about these changes (simply by mail)? Information is badly communicated and I hope there will be changes in this aspect too.

    Comment


    • #32
      Originally posted by jeny View Post
      In my point of view there are goods changes and i am happy to learn about this new version.
      But, why doesn't illumina make aware its users about these changes (simply by mail)?
      I'm sure they will be telling registered customers directly, but that may take a while to reach end users.
      Originally posted by jeny View Post
      Information is badly communicated and I hope there will be changes in this aspect too.
      As an outsider things are getting better - posting this announcement here on seqanswers.com is a positive step. Its a good way to reach a lot of developers and end users

      Comment


      • #33
        Originally posted by sklages View Post
        Hi Semyon,

        for the new GAII/HiSeq2000 runs I will surely use the software as intended, but as usual, other people read about CASAVA's capabilities/performance and want their datasets to be mapped and, very important, to be variant-called again. If the datasets are "old", we don't keep them online anymore, what is left in this case, are the user's FastQ files. That's why I am asking. The fastq files themselves should be enough for mapping and SNP calling!?

        cheers,
        Sven
        I see your point, but there still are some run specific files that are needed. Specifically, the Bustard summary.xml file is used in the generation of alignment statistics. A config file is needed to provide the alignment parameters, but that one is easy to make. I understand the desire to just go from FASTQ for older data sets and will try to think of a path to do this in an easy way.

        Thanks,
        Semyon

        Comment


        • #34
          nice

          it is really nice that illumina brings updates regularly
          Last edited by rajasereddy; 02-05-2011, 11:42 PM.

          Comment


          • #35
            Bustardsumary.xml

            Dear skruglyak
            After upgrade is there any change in the path of bustardsummary.xml file? After upgrade we are unable to locate the file though we are able to get all the data. What would be the possible reason?

            Thanks in advance
            rajase

            Comment


            • #36
              Originally posted by rajasereddy View Post
              Dear skruglyak
              After upgrade is there any change in the path of bustardsummary.xml file? After upgrade we are unable to locate the file though we are able to get all the data. What would be the possible reason?

              Thanks in advance
              rajase
              Hi Rajase,

              some file locations will be different due to the new directory structure. I am a little confused by your post because we have not yet released the software, so I am not sure how you could have upgraded. Feel free to send me a message directly with your version numbers and details of the situation and I will try to help.

              thanks,

              Semyon

              Comment


              • #37
                .. well, that raises one simple question: when will 1.8 be released?

                cheers, Sven

                Comment


                • #38
                  Originally posted by sklages View Post
                  .. well, that raises one simple question: when will 1.8 be released?

                  cheers, Sven

                  Hi Sven,

                  we plan to release to several early access sites next week. We will use the release in our services group and also gather feedback from early access and do the wide release once the feedback is collected and addressed.

                  Thanks,
                  Semyon

                  Comment


                  • #39
                    Hi Seymon,

                    Are you guys changing anything in demultiplex process?Pretty confused to deal with the directories created during demultiplex process.
                    Thx.

                    Comment


                    • #40
                      Originally posted by aparna View Post
                      Hi Seymon,
                      Are you guys changing anything in demultiplex process?Pretty confused to deal with the directories created during demultiplex process.
                      Thx.
                      That's perfectly true! Good point ...
                      Well, ok, a little script will do data compiling for you, but nevertheless, it's unnecessarily confusing :-)

                      Sven

                      Comment


                      • #41
                        Originally posted by aparna View Post
                        Hi Seymon,

                        Are you guys changing anything in demultiplex process?Pretty confused to deal with the directories created during demultiplex process.
                        Thx.
                        Yes, we are changing the demultiplex process. The demultiplexing will happen along with the bcl conversion. The directories will simply be organized by sample name. Within each sample directory, you will have the the zipped fastq files for that sample only. The sample names will come from the sample sheet that you provide. An example of the directory structure is on page 6 of the pdf that I attached to the original psot.

                        Thanks,
                        Semyon

                        Comment


                        • #42
                          Thx.Thats refreshing.
                          I have another question to ask...about the qseq-mask. Right now I need to specify qseq-mask to get all 7 barcode basepairs reported in fastq files-yet If I want to do such analysis for only one/few lanes (some lanes Illumina 6 barcode nts and other lanes 7nt barcode indexed run),I got to break the pipeline to start the Gerald process manually for such lanes.
                          So my question is:

                          Can we configure the qseq-mask for specific lanes during demultiplex process itself and continue through Gerald without manually starting the process?


                          Thx

                          Comment


                          • #43
                            Originally posted by aparna View Post
                            Thx.Thats refreshing.
                            I have another question to ask...about the qseq-mask. Right now I need to specify qseq-mask to get all 7 barcode basepairs reported in fastq files-yet If I want to do such analysis for only one/few lanes (some lanes Illumina 6 barcode nts and other lanes 7nt barcode indexed run),I got to break the pipeline to start the Gerald process manually for such lanes.
                            So my question is:

                            Can we configure the qseq-mask for specific lanes during demultiplex process itself and continue through Gerald without manually starting the process?


                            Thx

                            If I am understanding your question correctly, I think that your use case should already work. If you qseq mask 7 bases in all lanes, but specify the index sequences in the sample sheet as appropriate - with 6 bases in some lanes and 7 in others, then the program should do what you want. Have you already tried this?

                            thanks,
                            Semyon

                            Comment


                            • #44
                              Sorry I forgot to mention that I am trying to perform alignment of indexed qseq files without
                              actually demultiplexing by supplying an empty formatted sample sheet (demultiplexing with pipeline sw is utterly confusing)and I depend on the barcode sequences reported in the fastq files for my downstream analysis.

                              what do you advise to perform demultiplex and Gerald (making use of make align=YES) for all lanes no matter what indexes I use.

                              Right now without qseq-mask I get 6 nts barcode reported in fastq read description lines.
                              But with qseq-mask option (Y# I7 or 8 y#), I need to perform analysis in different batches to kick off demultiplex+Gerald at once.

                              BTW Is Illumina planning to release more than 12 barcodes in near future?

                              Thx.

                              Comment


                              • #45
                                Originally posted by aparna View Post
                                Sorry I forgot to mention that I am trying to perform alignment of indexed qseq files without
                                actually demultiplexing by supplying an empty formatted sample sheet (demultiplexing with pipeline sw is utterly confusing)and I depend on the barcode sequences reported in the fastq files for my downstream analysis.

                                what do you advise to perform demultiplex and Gerald (making use of make align=YES) for all lanes no matter what indexes I use.

                                Right now without qseq-mask I get 6 nts barcode reported in fastq read description lines.
                                But with qseq-mask option (Y# I7 or 8 y#), I need to perform analysis in different batches to kick off demultiplex+Gerald at once.

                                BTW Is Illumina planning to release more than 12 barcodes in near future?

                                Thx.
                                Well, the 1.8 version should clear up the confusing directory structure you are currently facing. I don't know how to best process the data with the existing version if you don't want to use the demultiplexing script. I would be happy to put you in touch with tech support if you would like.
                                As for more bar codes, this is under development, but I am not the right person to comment on release time lines.

                                thanks,
                                Semyon

                                Comment

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