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#81 horizontal gene coverage

New
MOCAT
horizontal (1)
Medium
Defect
2018-02-12
2018-02-12
Peter Bazeley
No

Hello,
Do the horiztonal gene abundance files refer to horiztonal gene transfers? If so, are these from a database or do you have more info I can read about these?
Thank you for your assistance,
Peter Bazeley

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Tickets: #81

Discussion

  • MOCAT

    MOCAT - 2018-02-12

    No. These are the horizontal gene coverages (what fraction of the gene has
    coverage), which is not related of horizontal gene transfers.

    On Mon, Feb 12, 2018 at 05:25 Peter Bazeley theoark@users.sourceforge.net
    wrote:

    ** [tickets:#81] horizontal gene coverage**

    Status: New
    Labels: horizontal
    Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
    Last Updated: Mon Feb 12, 2018 04:25 AM UTC
    Owner: MOCAT

    Hello,
    Do the horiztonal gene abundance files refer to horiztonal gene transfers?
    If so, are these from a database or do you have more info I can read about
    these?
    Thank you for your assistance,
    Peter Bazeley

    Sent from sourceforge.net because you indicated interest in <
    https://sourceforge.net/p/mocat/tickets/81/>

    To unsubscribe from further messages, please visit <
    https://sourceforge.net/auth/subscriptions/>

    --
    Sent from my iPhone - apologies for any iCorrect mistakes.

     

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    Tickets: #81

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    • Peter Bazeley

      Peter Bazeley - 2018-02-21

      Do you have more details of how this is calculated? Is it just a proportion
      of the gene length that has any read alignment or is it weighted by the
      number of reads? I'm wondering how to interpret these. Thanks.

      On Mon, Feb 12, 2018 at 4:21 AM, MOCAT <mocat-pipeline@users.sourceforge.net

      wrote:

      No. These are the horizontal gene coverages (what fraction of the gene has
      coverage), which is not related of horizontal gene transfers.

      On Mon, Feb 12, 2018 at 05:25 Peter Bazeley theoark@users.sourceforge.net
      wrote:

      Status: New
      Labels: horizontal
      Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
      Last Updated: Mon Feb 12, 2018 04:25 AM UTC
      Owner: MOCAT

      Hello,
      Do the horiztonal gene abundance files refer to horiztonal gene transfers?
      If so, are these from a database or do you have more info I can read about
      these?
      Thank you for your assistance,
      Peter Bazeley

      Sent from sourceforge.net because you indicated interest in <
      https://sourceforge.net/p/mocat/tickets/81/>

      To unsubscribe from further messages, please visit <
      https://sourceforge.net/auth/subscriptions/>

      --
      Sent from my iPhone - apologies for any iCorrect mistakes.

      Status: New
      Labels: horizontal
      Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
      Last Updated: Mon Feb 12, 2018 04:25 AM UTC
      Owner: MOCAT

      Hello,
      Do the horiztonal gene abundance files refer to horiztonal gene transfers?
      If so, are these from a database or do you have more info I can read about
      these?
      Thank you for your assistance,
      Peter Bazeley

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/mocat/tickets/81/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

       

      Related

      Tickets: #81

      alternate

      • MOCAT

        MOCAT - 2018-02-21

        It's the porportion of the gene/contig/sequence that has at least 1x
        coverage, ie a read covering that piece. Very basic in that sense.

        Jens Roat Kultima, Ph.D.

        Computational Scientist
        Janssen Human Microbiome Institute
        Janssen Pharmaceuticals
        255 Main Street, 10th Floor
        Cambridge, MA 02142

        On Wed, Feb 21, 2018 at 11:38 AM, Peter Bazeley theoark@users.sourceforge.net wrote:

        Do you have more details of how this is calculated? Is it just a proportion
        of the gene length that has any read alignment or is it weighted by the
        number of reads? I'm wondering how to interpret these. Thanks.

        On Mon, Feb 12, 2018 at 4:21 AM, MOCAT <mocat-pipeline@users.
        sourceforge.net

        wrote:

        No. These are the horizontal gene coverages (what fraction of the gene
        has
        coverage), which is not related of horizontal gene transfers.

        On Mon, Feb 12, 2018 at 05:25 Peter Bazeley
        theoark@users.sourceforge.net
        wrote:

        Status: New
        Labels: horizontal
        Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
        Last Updated: Mon Feb 12, 2018 04:25 AM UTC
        Owner: MOCAT

        Hello,
        Do the horiztonal gene abundance files refer to horiztonal gene
        transfers?
        If so, are these from a database or do you have more info I can read
        about
        these?
        Thank you for your assistance,
        Peter Bazeley

        Sent from sourceforge.net because you indicated interest in <
        https://sourceforge.net/p/mocat/tickets/81/>

        To unsubscribe from further messages, please visit <
        https://sourceforge.net/auth/subscriptions/>

        --
        Sent from my iPhone - apologies for any iCorrect mistakes.

        Status: New
        Labels: horizontal
        Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
        Last Updated: Mon Feb 12, 2018 04:25 AM UTC
        Owner: MOCAT

        Hello,
        Do the horiztonal gene abundance files refer to horiztonal gene
        transfers?
        If so, are these from a database or do you have more info I can read
        about
        these?
        Thank you for your assistance,
        Peter Bazeley

        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/mocat/tickets/81/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        ** [tickets:#81] horizontal gene coverage**

        Status: New
        Labels: horizontal
        Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley
        Last Updated: Mon Feb 12, 2018 04:25 AM UTC
        Owner: MOCAT

        Hello,
        Do the horiztonal gene abundance files refer to horiztonal gene transfers?
        If so, are these from a database or do you have more info I can read about
        these?
        Thank you for your assistance,
        Peter Bazeley

        Sent from sourceforge.net because you indicated interest in <
        https://sourceforge.net/p/mocat/tickets/81/>

        To unsubscribe from further messages, please visit <
        https://sourceforge.net/auth/subscriptions/>

         

        Related

        Tickets: #81

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