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  1. Installing ChromoZoom on my own server

    I was trying to installing ChromoZoom on debian server. It went very smoothly following the README.

    I vagranted up a VM (chrome-1) and downloaded the hg19 track. I think It should be able to show on https://localhost:8080 as well. However, it was totally an empty website. I couldn't find any track to use.

    How could I do.

    Thanks!

    --
    WM

    1 vote
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      0 comments  ·  Admin →

    • Personal Genome SNP format

      Could the ucsc "Personal Genome SNP format" be added ? It is slightly different from the bed format and would be useful to view personal genomes. Thanks

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        0 comments  ·  Admin →

      • Does the windowing function work?

        Hi Support,

        What is windowing function? It seems to me, the windowing function doesn't work. Can you make sure it?

        I guess the windowing function is a normalization term based on maxmal/mean/minimal value of reads. Is it right?

        Thanks.

        1 vote
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          1 comment  ·  Admin →

        • Add other organisms?

          It would be great if we can load tracks for other organisms like Drosophila to this server!

          4 votes
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            2 comments  ·  Admin →

          • Provide Dropbox and other online drive storage systems (google drive, box.net etc)

            It would be great if you could allow the user to login to dropbox, google drive, box.net, etc.. and allow us to pick a file to display on the browser from those online storage systems.

            3 votes
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              1 comment  ·  Admin →
              under review  ·  Ted PakAdminTed Pak (ChromoZoom dev, chromozoom) responded

              Would it be possible to put these files in e.g. a Dropbox Public folder and use the public URLs? We’re not sure if this is more amenable than having ChromoZoom authenticate directly with all of these cloud services. With the Public URL method, there’s no concern that we would write to or delete files in the cloud. We will look into the APIs currently available, though.

              Edit: having taken a look at https://www.dropbox.com/developers/chooser, this might not be that difficult to do at all.

            • Provide a mechanism to save a session to collaborate with other people

              Implement the Session-style capability present in the UCSC genome browser...
              If storage is of concern (this could be avoided by allowing the user to login with online storage system credentials and saving the session there) - related to my other feedback suggestion )https://chromozoom.uservoice.com/forums/158554-general/suggestions/3891926-provide-dropbox-and-other-online-drive-storage-sys)

              3 votes
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                1 comment  ·  Admin →
                under review  ·  Ted PakAdminTed Pak (ChromoZoom dev, chromozoom) responded

                I’m trying to think about the best way to do this. Is there any way that it can already be done using the “Link to this view:” link, assuming all your files being loaded from URLs and not your computer? Our main issue with saving the tracks themselves is that we are concerned we will rapidly run out of space without per-user quotas, which will require a lot of support overhead.

              • Add an Ensembl genes track

                Since you have the UCSC and RefSeq genes already, why not add the Ensembl genes as well?
                Also, I notice you're using hg19 as the assembly, but the GRC official name is GRCh37. How about labelling it as hg19/GRCh37 as UCSC does?
                Nice work! It's fast, simple, and pretty!

                4 votes
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                  0 comments  ·  Admin →

                • If the browser's zoom is not 100%, mouse navigation breaks

                  If the browser's zoom is not 100%, interactions with the mouse do not work correctly.

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                    0 comments  ·  Admin →

                  • Visualize list of genes and its position for certain region

                    see example: http://cccb.dfci.harvard.edu/cbgb/

                    2 votes
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                      0 comments  ·  Admin →

                    • Add S.cerevisiae genetic variation from the SGRP project

                      There is data on common variants available from the Sanger website as well as Liti et al. 2009.

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                        1 comment  ·  Admin →
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