454 RNAseq (human) data submission for UCSC

[Hagen Tilgner]

Dear all,

we have two data sets (454 RNAseq in K562 and HelaS3, median >500bp length, 4-5 million reads in each data set). I tried to follow Kate's instructions on how to create a hub. The hub-check seems to indicate that things are fine (see below). Would it be possible for someone on your end to double-check this ?

nuvol:UCSC_upload htilgner$ pwd
/Users/htilgner/data/454yale_lukasHabbegger/v1/analysis/K562/generalMapping/all32lanes/analyse1.v0.2/UCSC_upload
nuvol:UCSC_upload htilgner$ date
Thu Aug 15 11:34:26 PDT 2013
nuvol:UCSC_upload htilgner$ ./hubCheck http://www.stanford.edu/~htilgner/2012_454paper/data/hub.txt
nuvol:UCSC_upload htilgner$

All the best
Hagen

---------- Forwarded message ----------
From: Kate Rosenbloom <ka...@soe.ucsc.edu>
Date: Thu, Aug 15, 2013 at 9:36 AM
Subject: Re: online accessible (unpublished) draft & data for UCSC ?
To: Hagen Tilgner <hagen.u...@gmail.com>


Hi Hagen,

You'll need to add http:// prefix to your url.
You'll get quickest response to questions by contacting the Genome Browser mailing list directly -- they usually have the right answer for you same day!   Mail gen...@soe.ucsc.edu. You can also search on archived questions, see Contacts page:
http://genome.ucsc.edu/contacts.html

A beautiful example of hub configuration and documentation is the ENCODE Analysis hub:

http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/genomes.txt
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/uniformTfbs.html
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/uniformRNA.html

(I'd only change the number of tracks visible by default -- it's too many (slow to load and overwhelming to users) -- but this will not be a problem for your data).

Often the paper abstract is useful as a start for the 'Description' section -- summary of what data is and why it is of interest.  Methods should have a bit more detail.  Definitely include a contact.  Assume broad audience of students as well as researchers, and don't assume knowledge of NGS or even genomics (e.g. bench biologists).


  Cheers,
     Kate


On 8/14/13 8:56 PM, Hagen Tilgner wrote:

Dear Kate,

... me again, sorry! Making the hub. I have two questions ... could you  put me in touch with someone who handles these hubs ?


my questions are

1) when doing the hub-check, I get this message (although when pasting the below url into a browser, I can see it)

nuvol:UCSC_upload htilgner$ ./hubCheck www.stanford.edu/~htilgner/2012_454paper/data/hub.txt <http://www.stanford.edu/%7Ehtilgner/2012_454paper/data/hub.txt>
Errors with hub at 'www.stanford.edu/~htilgner/2012_454paper/data/hub.txt <http://www.stanford.edu/%7Ehtilgner/2012_454paper/data/hub.txt>'
No such file or directory
Can't open www.stanford.edu/~htilgner/2012_454paper/data/hub.txt <http://www.stanford.edu/%7Ehtilgner/2012_454paper/data/hub.txt> to read

nuvol:UCSC_upload htilgner$


2) Is there an example html file, which I could modify for the data-description?



All the best
Hagen





On Tue, Aug 13, 2013 at 9:16 AM, Hagen Tilgner <hagen.u...@gmail.com <mailto:hagen.u.tilgner@gmail.com>> wrote:

    Dear Kate,

    - I got the link through google scholar (it appeared as citing one
    of my earlier papers). It is the second paper on this link:

    http://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0,5&cites=12858534513556848196&scipsc=&q=&scisbd=1

    - will look at the link now for the UCSC hub now.

    All the best
    Hagen


    On Tue, Aug 13, 2013 at 9:11 AM, Kate Rosenbloom
    <ka...@soe.ucsc.edu <mailto:ka...@soe.ucsc.edu>> wrote:

        Hi Hagen,

        Can you tell me how you obtained this link ?  It appears to be
        a backup of a retired wiki.   We are currently in the process
        of work at .sdsc.edu <http://sdsc.edu>, and this is likely an
        interim directory used by our system administrators.

        Regarding the data -- long reads and transcript assembly for
        ENCODE cell lines are long-awaited!  Best way to move forward
        to make it more accessible is to create a browser data hub,
        which is relatively easy.  The basics are reformatting your
        data in indexed binary format (e.g. BAM for reads, BED12 for
        transcript models), posting to a web-accessible location, and
        creating a few text files of metadata.  More info here:

        http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

        Cheers,
            Kate Rosenbloom
            UCSC Genome Bioinformatics
            ENCODE DCC


        On 8/12/13 12:27 PM, Hagen Tilgner wrote:

            Dear Dr. Rosenbloom,

            - an old draft of a paper that we are still working on (it
            was originally meant to go with ENCODE, but finally did
            not), appeared on the ENCODE pages (please see the link
            before). Woudl it be possible to take this off ? Could you
            put me in touch with who might be able to do that ?

            ftp://hgdownload-sd.sdsc.edu/cbsebackup1/genomewiki/scratch/backWiki/files/EncodeDCC/2/2f/GRC008.chromatin_splicing_Guigo.pdf


            - also, we recently published a paper using 454 for RNAseq
            in the ENCODE cell-lines K562 and HelaS3 (PMID:23450794)
            ... these reads are basically next generation ESTs and
            usually span many exons. Would you be interested in
            housing them at the USCS browser (we have gzipped gff/gtf
            filse, which are around ~90Mbyte and contain almost 2
            million spliced alignments).


            All the best
            Hagen

[Luvina Guruvadoo]

Hi Hagen,

Thanks for contacting us. Your track hub appears to be loading just fine. May I point out that for performance reasons, UCSC checks the time stamps on hub files every 300 seconds, which can result in a 5-minute delay between the time a hub file is updated and the change appears on the Genome Browser. You can read more about this in our track hub help page here:
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Debug

I hope this helps. If you have further questions or comments, please reply to gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

--
 

[Hagen Tilgner]

Dear engineers,

- would it be possible to register our hub at the UCSC browser ?

- The hub.txt is at http://www.stanford.edu/~htilgner/2012_454paper/data/hub.txt .

- a hub-check gave no erros

nuvol:UCSC_upload htilgner$ pwd
/Users/htilgner/data/454yale_lukasHabbegger/v1/analysis/K562/generalMapping/all32lanes/analyse1.v0.2/UCSC_upload
nuvol:UCSC_upload htilgner$ date
Thu Aug 15 11:34:26 PDT 2013
nuvol:UCSC_upload htilgner$ ./hubCheck http://www.stanford.edu/~htilgner/2012_454paper/data/hub.txt
nuvol:UCSC_upload htilgner$

- please tell me as soon as it is available. I would love to check quickly to make sure that I have not introduced any error wile converting to the formats for the hub.

All th ebest

Hagen

---------- Forwarded message ----------
From: Luvina Guruvadoo <luv...@soe.ucsc.edu>
Date: Wed, Aug 21, 2013 at 7:44 PM
Subject: Re: [genome] 454 RNAseq (human) data submission for UCSC
To: Hagen Tilgner <hagen.u...@gmail.com>

Hi Hagen,

I'm sorry, but we do not provide support over the phone. If you are interested in registering a track hub with UCSC, please see the following help page: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Register. Please send your request to gen...@soe.ucsc.edu so that one of our engineers may assist you. Thanks for your understanding in this matter.

Regards,

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

On 8/21/2013 5:16 PM, Hagen Tilgner wrote:

Dear Luvina,

could I call you today or tomorrow ? I actually cannot see our data on teh UCSC browser.

ALl the best
Hagen

[Luvina Guruvadoo]

Hi Hagen,

Thanks for your interest in registering a public hub with UCSC. We have added your hub to the queue for review. In the meantime, we encourage you to have a look at our recommended guidelines for public hubs: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines. This will help quicken the process of making suggested improvements to your hub before it is approved.

We look forward to reviewing your hub and will contact you if we require additional information. If you have further questions or comments, please reply to gen...@soe.ucsc.edu.

Regards,
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

On 8/21/2013 8:24 PM, Hagen Tilgner wrote:

[Luvina Guruvadoo]

Hi Hagen,

Thanks for your interest in registering a public hub with UCSC. We have added your hub to the queue for review. In the meantime, we encourage you to have a look at our recommended guidelines for public hubs: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guideline. This will help quicken the process of making suggested improvements to your hub before it is approved.

We look forward to reviewing your hub and will contact you if we require additional information. If you have further questions or comments, please reply to gen...@soe.ucsc.edu.

Regards,
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

On 8/21/2013 8:24 PM, Hagen Tilgner wrote:

[Hagen Tilgner]

Dear UCSC-team,

could you let me know what the time-frame for this review is ? How many other reviews are in the queue before this one ?

Thank you & all the best

Hagen

[Luvina Guruvadoo]

Hi Hagen,

One of our engineers is taking a look at your hub now. We'll let you know once your hub has been released to our public site, probably within the next few days. Thanks for your patience.

If you have further questions or comments, please reply to gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group