Is it possible to get a look at your database schema?
> From: [email protected]
> Subject: Genome Digest, Vol 110, Issue 20
> To: [email protected]
> Date: Tue, 13 Mar 2012 16:32:58 -0700
>
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> Today's Topics:
>
> 1. Re: GENCODE Genes (Vanessa Kirkup Swing)
> 2. Re: Tables, tracks and groups in the table browser (Steve Heitner)
> 3. Re: Tables, tracks and groups in the table browser (Diego Pereira)
> 4. Default hg19 default tracks in genome-preview (Murphy, Kevin)
> 5. Re: Overlapping two custom tracks (robert kuhn)
> 6. Re: Overlapping two custom tracks (robert kuhn)
> 7. Re: A question about Chimpanzee (Vanessa Kirkup Swing)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 13 Mar 2012 12:01:42 -0700
> From: Vanessa Kirkup Swing <[email protected]>
> Subject: Re: [Genome] GENCODE Genes
> To: Maria Tropeano <[email protected]>
> Cc: [email protected]
> Message-ID:
> <capbuke5-f_1wbqthffi_rkvvyoe8pqehqov+v9xda+zjoh1...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Maria,
>
> The 3 latest versions (V7, V10, V11) of GENCODE Genes on hg19 are
> accessible from http://genome.ucsc.edu
>
>
> Here is a link to the track controls for the latest version of the GENCODE
> Genes track:
>
> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV11
>
>
> If you have further questions, please contact the mailing list:
> [email protected].
>
> Vanessa Kirkup Swing
> UCSC Genome Bioinformatics Group
>
>
>
> ---------- Forwarded message ----------
> From: Maria Tropeano <[email protected]>
> Date: Tue, Mar 13, 2012 at 3:56 AM
> Subject: [Genome] GENCODE Genes
> To: [email protected]
>
>
> Hi,
>
> The GENCODE Genes track is currently not available in the browser, however,
> since I would need to use it asap, I was wondering whether this is just as
> temporary problem and when it will be available again.
>
> Many thanks
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 13 Mar 2012 13:26:34 -0700
> From: "Steve Heitner" <[email protected]>
> Subject: Re: [Genome] Tables, tracks and groups in the table browser
> To: "'Diego Pereira'" <[email protected]>,
> <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello, Diego.
>
> In our ENCODE tracks, older tables often get revoked in favor of new tables
> when the data in them becomes obsolete or otherwise incorrect. These older
> tables still exist and show up in the "All Tables" list, but will not show
> up under the individual track listings in the Table Browser. For some
> non-ENCODE tracks such as the RefSeq Genes track, there are many supporting
> tables that are necessary, but not directly linked to the main table.
> Again, tables such as these will show up in the "All Tables" list, but not
> under the individual track listings. Examples such as these explain why the
> "All Tables" count does not exactly match the count of tables listed in the
> individual tracks.
>
> Please contact us again at [email protected] if you have any further
> questions.
>
> ---
> Steve Heitner
> UCSC Genome Bioinformatics Group
>
> -----Original Message-----
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Diego Pereira
> Sent: Wednesday, March 07, 2012 12:13 PM
> To: [email protected]
> Subject: [Genome] Tables, tracks and groups in the table browser
>
> Dear all,
> While comparing the hg19 tables, tracks and groups contained at the table
> browser I found some slight differences in tables numbers that called my
> attention.
> Under the track "alltables" there are 7524 tables.
> However, the total ammount of tables in all the other tracks (excluding the
> "alltracks" track of course) is 6900.
> By reviewing the names of the tables that are not included under the other
> tracks, I found that aprox 440 are wgEncode tables that should be present in
> other tracks.
> I checked the last email sent by Kate Rosenbloom to see wheter the reason
> for this was related with the categorization of the new releases, but that
> was not the case.
> The wgEncode tables not included under a specific track
> (theoretically) belong to different groups including expression and
> regulation.
> Therefore, I would like to ask, what is the reason they are not included in
> specific groups or tracks?
> I can send you the list upon your request.
> Regards,
> Diego
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 13 Mar 2012 15:30:55 -0500
> From: Diego Pereira <[email protected]>
> Subject: Re: [Genome] Tables, tracks and groups in the table browser
> To: [email protected]
> Cc: [email protected]
> Message-ID:
> <CABz1eoqwkERt=3edqd6uitoeku8+aefajd7wh6c1ysg-zg-...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Steve,
> Thank you very much for your answer.
> All the best,
> Diego
>
>
> El d?a 13 de marzo de 2012 15:26, Steve Heitner <[email protected]> escribi?:
> > Hello, Diego.
> >
> > In our ENCODE tracks, older tables often get revoked in favor of new tables
> > when the data in them becomes obsolete or otherwise incorrect. ?These older
> > tables still exist and show up in the "All Tables" list, but will not show
> > up under the individual track listings in the Table Browser. ?For some
> > non-ENCODE tracks such as the RefSeq Genes track, there are many supporting
> > tables that are necessary, but not directly linked to the main table.
> > Again, tables such as these will show up in the "All Tables" list, but not
> > under the individual track listings. ?Examples such as these explain why the
> > "All Tables" count does not exactly match the count of tables listed in the
> > individual tracks.
> >
> > Please contact us again at [email protected] if you have any further
> > questions.
> >
> > ---
> > Steve Heitner
> > UCSC Genome Bioinformatics Group
> >
> > -----Original Message-----
> > From: [email protected] [mailto:[email protected]] On
> > Behalf Of Diego Pereira
> > Sent: Wednesday, March 07, 2012 12:13 PM
> > To: [email protected]
> > Subject: [Genome] Tables, tracks and groups in the table browser
> >
> > Dear all,
> > While comparing the hg19 tables, tracks and groups contained at the table
> > browser I found some slight differences in tables numbers that called my
> > attention.
> > Under the track "alltables" there are 7524 tables.
> > However, the total ammount of tables in all the other tracks (excluding the
> > "alltracks" track of course) is 6900.
> > By reviewing the names of the tables that are not included under the other
> > tracks, I found that aprox 440 are wgEncode tables that should be present in
> > other tracks.
> > I checked the last email sent by Kate Rosenbloom to see wheter the reason
> > for this was related with the categorization of the new releases, but that
> > was not the case.
> > The wgEncode tables not included under a specific track
> > (theoretically) belong to different groups including expression and
> > regulation.
> > Therefore, I would like to ask, what is the reason they are not included in
> > specific groups or tracks?
> > I can send you the list upon your request.
> > Regards,
> > Diego
> > _______________________________________________
> > Genome maillist ?- [email protected]
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> >
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 13 Mar 2012 17:35:00 -0400
> From: "Murphy, Kevin" <[email protected]>
> Subject: [Genome] Default hg19 default tracks in genome-preview
> To: "[email protected]" <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> I notice that there are a number of additions to the list of default tracks
> in the genome-preview instance when using hg19.
>
> Are these going to persist when the release is made public?
>
> Is the theory to introduce users to new tracks and let users hide the tracks
> if they are not interested?
>
> Thanks,
> Kevin Murphy
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 13 Mar 2012 15:27:21 -0700
> From: robert kuhn <[email protected]>
> Subject: Re: [Genome] Overlapping two custom tracks
> To: Amelie Baud <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello, Amelie,
>
> If I understand your question correctly, you are asking if
> it is possible to superimpose two tracks o the same set of
> axes for direct comparison?
>
> We agree that it would be great to be able to do that. That
> capability is in place for our resident tracks, but was only
> recently implemented. It is on our list of things to do to make
> the functionality available for Custom Tracks, but I cannot say
> when we be able to roll that out.
>
> You may be interested in the Track Hub system which gives you
> the much of the same capability for your own tracks that we have
> for our resident tracks. Please read about it here:
>
> http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
>
> to see if it suits your needs.
>
> You can see the overlay feature in operation in some of the
> Summary tracks in the Epigenomics Roadmap tracks on the hub
> page:
>
> http://genome.ucsc.edu/cgi-bin/hgHubConnect
>
> regards,
>
> --b0b kuhn
> ucsc genome bioinformatics group
>
>
> On 3/12/2012 3:18 AM, Amelie Baud wrote:
> > Dear all,
> >
> > Is it possible to overlap two custom tracks, so that the values on the
> > y-axis can be compared for a given position on the x-axis (position on the
> > chromsome)? That would be very helpful.
> >
> > Best wishes,
> >
> > Amelie
> >
> >
> > _______________________________________________
> > Genome maillist - [email protected]
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 13 Mar 2012 15:31:06 -0700
> From: robert kuhn <[email protected]>
> Subject: Re: [Genome] Overlapping two custom tracks
> To: Amelie Baud <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello, again, Amelie,
>
> Here is a previously answered question from the list that
> fills in more detail about the hubs:
>
> https://lists.soe.ucsc.edu/pipermail/genome/2011-August/026651.html
>
> regards,
>
> --b0b kuhn
>
> On 3/13/2012 3:27 PM, robert kuhn wrote:
> > Hello, Amelie,
> >
> > If I understand your question correctly, you are asking if
> > it is possible to superimpose two tracks o the same set of
> > axes for direct comparison?
> >
> > We agree that it would be great to be able to do that. That
> > capability is in place for our resident tracks, but was only
> > recently implemented. It is on our list of things to do to make
> > the functionality available for Custom Tracks, but I cannot say
> > when we be able to roll that out.
> >
> > You may be interested in the Track Hub system which gives you
> > the much of the same capability for your own tracks that we have
> > for our resident tracks. Please read about it here:
> >
> > http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
> >
> > to see if it suits your needs.
> >
> > You can see the overlay feature in operation in some of the
> > Summary tracks in the Epigenomics Roadmap tracks on the hub
> > page:
> >
> > http://genome.ucsc.edu/cgi-bin/hgHubConnect
> >
> > regards,
> >
> > --b0b kuhn
> > ucsc genome bioinformatics group
> >
> >
> > On 3/12/2012 3:18 AM, Amelie Baud wrote:
> >> Dear all,
> >>
> >> Is it possible to overlap two custom tracks, so that the values on the
> >> y-axis can be compared for a given position on the x-axis (position on
> >> the chromsome)? That would be very helpful.
> >>
> >> Best wishes,
> >>
> >> Amelie
> >>
> >>
> >> _______________________________________________
> >> Genome maillist - [email protected]
> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 13 Mar 2012 16:32:54 -0700
> From: Vanessa Kirkup Swing <[email protected]>
> Subject: Re: [Genome] A question about Chimpanzee
> To: Arthur Zhou <[email protected]>
> Cc: [email protected]
> Message-ID:
> <capbuke5ow0-3v0yxyqcsqxph+vg-7ogybnptqjsnmhx2zzh...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Arthur,
>
> Unfortunately, we don't host segmental duplication data for chimp. The
> following papers may be of interest to you:
>
> Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD,
> Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human
> genome <http://www.ncbi.nlm.nih.gov/pubmed/12169732?dopt=Abstract>. *
> Science.* 2002 Aug 9;297(5583):1003-7.
>
> Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental
> duplications: organization and impact within the current human genome
> project
> assembly<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11381028&dopt=Abstract>.
> *Genome Res.* 2001 Jun;11(6):1005-17.
>
>
> If you have further questions, please contact the mailing list:
> [email protected].
>
> Vanessa Kirkup Swing
> UCSC Genome Bioinformatics Group
>
> ---------- Forwarded message ----------
> From: Arthur Zhou <[email protected]>
> Date: Tue, Mar 13, 2012 at 1:32 AM
> Subject: [Genome] A question about Chimpanzee
> To: [email protected]
>
>
> Dear Sir,
>
> I hope you could tell me where to download the segmental duplications data
> of chimpanzee. For I've search the
> http://hgdownload.cse.ucsc.edu/downloads.html#chimp but I cannot find it.
> Thank so much if you have time to reply.
>
> Sincerely
> Arthur
>
> --
> Regards!
>
> Zhou Weichen
>
> MOE Key Laboratory of Contemporary Anthropology(Fudan University)
>
> School of Life-science at Fudan University
>
> 220# Handan Road, Shanghai(200433)
>
> P.R.China.
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
> ------------------------------
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
> End of Genome Digest, Vol 110, Issue 20
> ***************************************
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