Valid 'view_mode' options in quickload

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Chris
2014-06-03
2014-06-12
  • Chris

    Chris - 2014-06-03

    Hi,

    In the annots.xml file what are valid 'view_mode' settings? Only 'depth' is in the documentation and it doesn't seem to change the default. Ideally, I'd like be able to view Pileup mismatch graphs, but the ability to choose any option other than the default for BAM files would be great.
    Thanks,

    Chris

     
  • ktsuttlemyre

    ktsuttlemyre - 2014-06-04

    Hello Chris,

    The "view_mode" attribute for files tags in annots.xml appears to be disabled.

    I will bring this up with the development team and get back to you on the details.

    Thanks for bringing this to our attention!

    -Kyle

     
    Last edit: Ann E. Loraine 2014-06-10
  • Chris

    Chris - 2014-06-06

    OK. Thanks.

     
  • Mason Meyer

    Mason Meyer - 2014-06-10

    Hi Chris,

    To follow up on Kyle's comment:

    You can view a pileup or other types of graphs by right-clicking a BAM file (read alignments) track label and selecting the Track Operations menu.

    See:

    https://wiki.transvar.org/confluence/display/igbman/Creating+Graph+Tracks+from+Annotation+Tracks

    The "view mode" feature documented in the User's Guide is obsolete, and we've removed it from the documentation.

    Sorry for the confusion. If you have other questions, please let us know!

    Best,

    Mason & Ann

     
    Last edit: Ann E. Loraine 2014-06-10
  • Chris

    Chris - 2014-06-12

    Hi Mason & Ann,

    Yes, I am aware of how to generate the pileup manually. I was interested in finding out how to do it automatically.

    Thanks for letting me know that 'view mode' is obsolete. I'll not use it.
    Cheers,

    Chris

     

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