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  • #31
    MapView 3.1.2 is released!

    If you have some suggestions or bugs, please post here! Thanks!

    Comment


    • #32
      Thanks baohua.
      Whats the changelog? Is there a command-line version using x-windows maybe?
      --
      bioinfosm

      Comment


      • #33
        indels

        First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

        Comment


        • #34
          Thanks! bioinform! Sorry, there is not a command-line version using x-windows now.

          Originally posted by bioinfosm View Post
          Thanks baohua.
          Whats the changelog? Is there a command-line version using x-windows maybe?

          Comment


          • #35
            Thanks for your reply! MapView 3.1.2 only support for visualization of ungapped alignment. We will add the function of gapped and spliced alignment later.

            Originally posted by garwuf View Post
            First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

            Comment


            • #36
              I tried to run MapView using Mono on a Mac OS X 10.5. It started, displayed the window briefly, the crashed with this error:

              System.NotImplementedException: The requested feature is not implemented.
              at System.Windows.Forms.XplatUICarbon.get_CursorSize () [0x00000]
              at System.Windows.Forms.XplatUI.get_CursorSize () [0x00000]
              at System.Windows.Forms.SystemInformation.get_CursorSize () [0x00000]
              at MapView.Form1.abmmeKAlo (System.Object , System.EventArgs ) [0x00000]
              at System.Windows.Forms.Form.OnLoad (System.EventArgs e) [0x00000]
              at System.Windows.Forms.Form.OnLoadInternal (System.EventArgs e) [0x00000]
              Segmentation fault

              Any suggestions? Thanks.

              Comment


              • #37
                I ran the software on Windows, and was able to get it running. However, after converting a MAQ alignment to MVF, when I load the MVF file, I get an error:

                Arithmetic operation resulted in an overflow.

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                • #38
                  The paper is published on Bioinformaitcs.

                  MapView: visualization of short reads alignment on a desktop computer

                  Comment


                  • #39
                    congrats baohua!
                    It would be great if you could keep a running log of changes for newer versions
                    --
                    bioinfosm

                    Comment


                    • #40
                      Originally posted by lh3 View Post
                      . I know it is trivial to convert SAM/BAM to MVF, but given the large amount of data (maybe >1TB data), most users would prefer viewing the alignment directly rather than duplicate them again.
                      I have to reiterate the point lh3 is making. SAM/BAM format would be great if you could support it, since even people outside of 1000 genomes have generated 100's of GBs of data in SAM/BAM. Also, paired end info, indels, quality scores, complex references, and the ability to add arbitrary annotation and post-alignment "tracks" (maybe interact with a backend database?) would be the killer application.

                      Comment


                      • #41
                        Hello,

                        I'm using Mapview and it works fine. A feature that could be useful to be included is to show the reference and its coverage. Not on top like now, but maybe as a separate feature, having the reference presented as a bar and the parts which are covered could have a certain color (maybe depending on the amount of reads covering that region). In this way I could compare my annotation shown in a GenomeBrowser with the mapping of my exon reads on the reference.

                        Many thanks

                        Comment


                        • #42
                          The new version is being planned. We are discussing the new features.
                          SAM/BAM format will be supported.
                          A command line version will be available.
                          ... ...
                          WJW-Davy
                          HomePage: http://hi.baidu.com/wjwdavy
                          Download Center: https://sites.google.com/site/wjwdavy/

                          Comment


                          • #43
                            Hello,
                            is there a way to export the SNP list to a flat file? Like the one maq produces?

                            Thanks!

                            Comment


                            • #44
                              Originally posted by Drake View Post
                              Hello,
                              is there a way to export the SNP list to a flat file? Like the one maq produces?

                              Thanks!
                              3.1.4 [2009.5.2]

                              Text can be copyed from SNP list.
                              MVR file can be converted to text file. The SNP list can be exported to a flat file.
                              Last edited by WJW-Davy; 05-01-2009, 07:47 PM.
                              WJW-Davy
                              HomePage: http://hi.baidu.com/wjwdavy
                              Download Center: https://sites.google.com/site/wjwdavy/

                              Comment


                              • #45
                                to Drake

                                <i>is there a way to export the SNP list to a flat file? Like the one maq produces?</i>

                                I'm using HyperSnap (screen capture program) for that. It has text capture mode, can get text from scrolling windows and output it in tab-delimited format. I guess SnagIt also might do something like that. Unfortunately, both these software pieces are commercial.

                                Comment

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