how to display bigWig data

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how to display bigWig data

Maxim-4
Hi,

In order to test whether I was able to overcome my problems to display
wiggle data in an appropriate way I decided to test the available
bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.

Next I set up a human genome database on my MySQL backend and
everything works like a charm.

Unfortunately the bigWig data is not showing up, basically there is
nothing visible, not even an empty track lane. What I did:

I converted a vstep wiggle file using the wigToBigWig application. The
file is ok as I can use it on UCSC Browser, additonally I tested it in
a Perl-script using the Bio::DB::BigWig module and I was able to
extract some data with it.

Then I added those lines to my configuration file:
[BigWig:database]

 db_adaptor    = Bio::DB::BigWig
 db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig


 [BigWigIntervals]
 feature  = summary
 database = BigWig
 glyph    = wiggle_whiskers
 min_score = 0
 max_score = 80
 key       = test bigWig

Does anyone have clue what I might be doing wrong?

Maxim

P.S: Apache error log says:
--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

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Re: how to display bigWig data

Timothy Parnell
Hi Maxim,
I don't see anything wrong with your configuration stanzas, they match what I use. The fact that you can read the bigwig files with a custom script is good. So this makes me wonder whether the permissions are set correctly on the bigwig file; obviously you can read it, but is the file and directory tree readable by the apache user?
Tim

--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112


On 6/10/10 9:06 AM, "Maxim" <[hidden email]> wrote:

Hi,

In order to test whether I was able to overcome my problems to display
wiggle data in an appropriate way I decided to test the available
bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.

Next I set up a human genome database on my MySQL backend and
everything works like a charm.

Unfortunately the bigWig data is not showing up, basically there is
nothing visible, not even an empty track lane. What I did:

I converted a vstep wiggle file using the wigToBigWig application. The
file is ok as I can use it on UCSC Browser, additonally I tested it in
a Perl-script using the Bio::DB::BigWig module and I was able to
extract some data with it.

Then I added those lines to my configuration file:
[BigWig:database]

 db_adaptor    = Bio::DB::BigWig
 db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig


 [BigWigIntervals]
 feature  = summary
 database = BigWig
 glyph    = wiggle_whiskers
 min_score = 0
 max_score = 80
 key       = test bigWig

Does anyone have clue what I might be doing wrong?

Maxim

P.S: Apache error log says:
--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
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Re: how to display bigWig data

nicki
In reply to this post by Maxim-4
Hi Maxim

Try adding the line

category       = BigWigs

into the stanza, eg:

[BigWigIntervals]
category       = BigWigs
feature  = summary
database = BigWig
glyph    = wiggle_whiskers
min_score = 0
max_score = 80
key       = test bigWig


Nicki

---------------------
Nicki Gray
MRC Molecular Haematology Unit
Weatherall Institute of Molecular Medicine
John Radcliffe Hospital
Oxford, OX3 9DS
01865 222434

On 10 Jun 2010, at 16:06, Maxim wrote:

> Hi,
>
> In order to test whether I was able to overcome my problems to display
> wiggle data in an appropriate way I decided to test the available
> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>
> Next I set up a human genome database on my MySQL backend and
> everything works like a charm.
>
> Unfortunately the bigWig data is not showing up, basically there is
> nothing visible, not even an empty track lane. What I did:
>
> I converted a vstep wiggle file using the wigToBigWig application. The
> file is ok as I can use it on UCSC Browser, additonally I tested it in
> a Perl-script using the Bio::DB::BigWig module and I was able to
> extract some data with it.
>
> Then I added those lines to my configuration file:
> [BigWig:database]
>
> db_adaptor    = Bio::DB::BigWig
> db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>
>
> [BigWigIntervals]
> feature  = summary
> database = BigWig
> glyph    = wiggle_whiskers
> min_score = 0
> max_score = 80
> key       = test bigWig
>
> Does anyone have clue what I might be doing wrong?
>
> Maxim
>
> P.S: Apache error log says:
> --------------------- WARNING ---------------------
> MSG: Got a sequence with no letters in it cannot guess alphabet
> ---------------------------------------------------
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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Nicki Gray
MRC Molecular Haematology Unit
Weatherall Institute of Molecular Medicine
John Radcliffe Hospital
Oxford, UK, OX3 9DS
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Re: how to display bigWig data

Lincoln Stein
In reply to this post by Maxim-4
Hi,

This should work. I second the opinion that it is likely a permissions issue for the web server. Do you see any error messages in the server error log?

Lincoln

On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
Hi,

In order to test whether I was able to overcome my problems to display
wiggle data in an appropriate way I decided to test the available
bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.

Next I set up a human genome database on my MySQL backend and
everything works like a charm.

Unfortunately the bigWig data is not showing up, basically there is
nothing visible, not even an empty track lane. What I did:

I converted a vstep wiggle file using the wigToBigWig application. The
file is ok as I can use it on UCSC Browser, additonally I tested it in
a Perl-script using the Bio::DB::BigWig module and I was able to
extract some data with it.

Then I added those lines to my configuration file:
[BigWig:database]

 db_adaptor    = Bio::DB::BigWig
 db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig


 [BigWigIntervals]
 feature  = summary
 database = BigWig
 glyph    = wiggle_whiskers
 min_score = 0
 max_score = 80
 key       = test bigWig

Does anyone have clue what I might be doing wrong?

Maxim

P.S: Apache error log says:
--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: how to display bigWig data

Maxim-4
Hi,

I changed everything according to the above suggestions (permissions,
extra line in interval stanza). No improvement!

Apache error log says:

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

May it be that GBrowse does not know about the Bio::DB::BigWig
adapter? I think I first installed GBrowse and then the BigWig module!
May this be the reason?

Maxim

2010/6/10 Lincoln Stein <[hidden email]>:

> Hi,
> This should work. I second the opinion that it is likely a permissions issue
> for the web server. Do you see any error messages in the server error log?
> Lincoln
>
> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>
>> Hi,
>>
>> In order to test whether I was able to overcome my problems to display
>> wiggle data in an appropriate way I decided to test the available
>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>
>> Next I set up a human genome database on my MySQL backend and
>> everything works like a charm.
>>
>> Unfortunately the bigWig data is not showing up, basically there is
>> nothing visible, not even an empty track lane. What I did:
>>
>> I converted a vstep wiggle file using the wigToBigWig application. The
>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>> a Perl-script using the Bio::DB::BigWig module and I was able to
>> extract some data with it.
>>
>> Then I added those lines to my configuration file:
>> [BigWig:database]
>>
>>  db_adaptor    = Bio::DB::BigWig
>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>
>>
>>  [BigWigIntervals]
>>  feature  = summary
>>  database = BigWig
>>  glyph    = wiggle_whiskers
>>  min_score = 0
>>  max_score = 80
>>  key       = test bigWig
>>
>> Does anyone have clue what I might be doing wrong?
>>
>> Maxim
>>
>> P.S: Apache error log says:
>> --------------------- WARNING ---------------------
>> MSG: Got a sequence with no letters in it cannot guess alphabet
>> ---------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: how to display bigWig data

Lincoln Stein
In reply to this post by nicki
This shouldn't do anything.

Lincoln

On Thu, Jun 10, 2010 at 12:08 PM, Nicki Gray <[hidden email]> wrote:
Hi Maxim

Try adding the line

category       = BigWigs

into the stanza, eg:

[BigWigIntervals]
category       = BigWigs
feature  = summary
database = BigWig
glyph    = wiggle_whiskers
min_score = 0
max_score = 80
key       = test bigWig


Nicki

---------------------
Nicki Gray
MRC Molecular Haematology Unit
Weatherall Institute of Molecular Medicine
John Radcliffe Hospital
Oxford, OX3 9DS
01865 222434

On 10 Jun 2010, at 16:06, Maxim wrote:

> Hi,
>
> In order to test whether I was able to overcome my problems to display
> wiggle data in an appropriate way I decided to test the available
> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>
> Next I set up a human genome database on my MySQL backend and
> everything works like a charm.
>
> Unfortunately the bigWig data is not showing up, basically there is
> nothing visible, not even an empty track lane. What I did:
>
> I converted a vstep wiggle file using the wigToBigWig application. The
> file is ok as I can use it on UCSC Browser, additonally I tested it in
> a Perl-script using the Bio::DB::BigWig module and I was able to
> extract some data with it.
>
> Then I added those lines to my configuration file:
> [BigWig:database]
>
> db_adaptor    = Bio::DB::BigWig
> db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>
>
> [BigWigIntervals]
> feature  = summary
> database = BigWig
> glyph    = wiggle_whiskers
> min_score = 0
> max_score = 80
> key       = test bigWig
>
> Does anyone have clue what I might be doing wrong?
>
> Maxim
>
> P.S: Apache error log says:
> --------------------- WARNING ---------------------
> MSG: Got a sequence with no letters in it cannot guess alphabet
> ---------------------------------------------------
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: how to display bigWig data

Lincoln Stein
In reply to this post by Maxim-4
That error message is coming from something else, like the GC content track, and not from bigwig.  I really do not understand what is going on. If the bigwig file permissions are wrong, then you should see an error about being unable to open the file. If the adaptor module cannot be found, you should get a very verbose error complaining that the database adaptor is missing.

The installation order shouldn't matter; nor should the "category" option, which simply changes where the track label is displayed in the track table.

Are other people on this list using the BigWig adaptor successfully?

Lincoln

On Fri, Jun 11, 2010 at 5:28 AM, Maxim <[hidden email]> wrote:
Hi,

I changed everything according to the above suggestions (permissions,
extra line in interval stanza). No improvement!

Apache error log says:

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

May it be that GBrowse does not know about the Bio::DB::BigWig
adapter? I think I first installed GBrowse and then the BigWig module!
May this be the reason?

Maxim

2010/6/10 Lincoln Stein <[hidden email]>:
> Hi,
> This should work. I second the opinion that it is likely a permissions issue
> for the web server. Do you see any error messages in the server error log?
> Lincoln
>
> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>
>> Hi,
>>
>> In order to test whether I was able to overcome my problems to display
>> wiggle data in an appropriate way I decided to test the available
>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>
>> Next I set up a human genome database on my MySQL backend and
>> everything works like a charm.
>>
>> Unfortunately the bigWig data is not showing up, basically there is
>> nothing visible, not even an empty track lane. What I did:
>>
>> I converted a vstep wiggle file using the wigToBigWig application. The
>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>> a Perl-script using the Bio::DB::BigWig module and I was able to
>> extract some data with it.
>>
>> Then I added those lines to my configuration file:
>> [BigWig:database]
>>
>>  db_adaptor    = Bio::DB::BigWig
>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>
>>
>>  [BigWigIntervals]
>>  feature  = summary
>>  database = BigWig
>>  glyph    = wiggle_whiskers
>>  min_score = 0
>>  max_score = 80
>>  key       = test bigWig
>>
>> Does anyone have clue what I might be doing wrong?
>>
>> Maxim
>>
>> P.S: Apache error log says:
>> --------------------- WARNING ---------------------
>> MSG: Got a sequence with no letters in it cannot guess alphabet
>> ---------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: how to display bigWig data

Timothy Parnell
Lincoln,
Yes, I've been using the BigWig adaptor successfully. I have only used it for a few tracks so far in a development setting, but I've found it to be quite robust over the wiggle adaptor (see an earlier thread of mine). I'm in the process of converting most of my data to this and the SeqFeature::Store database, migrating from the old (...slow...) Bio::DB::GFF databases, so I'll be able to put it through its paces in another week or two.

Maxim,
Some other questions.
Are the chromosome seq_ids identical between the SeqFeature::Store database and the bigwig file?
Are the stanza titles unique in the conf file?
Are you able to see other tracks, or is it only the bigwig track that won't display?
Are you able to display other data using the xyplot family of adaptors? Say, data stored directly in the SeqFeature::Store database directly, or from the wiggle adaptor?

Tim
--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112



On 6/11/10 9:58 AM, "Lincoln Stein" <[hidden email]> wrote:

That error message is coming from something else, like the GC content track, and not from bigwig.  I really do not understand what is going on. If the bigwig file permissions are wrong, then you should see an error about being unable to open the file. If the adaptor module cannot be found, you should get a very verbose error complaining that the database adaptor is missing.

The installation order shouldn't matter; nor should the "category" option, which simply changes where the track label is displayed in the track table.

Are other people on this list using the BigWig adaptor successfully?

Lincoln

On Fri, Jun 11, 2010 at 5:28 AM, Maxim <[hidden email]> wrote:
Hi,

I changed everything according to the above suggestions (permissions,
extra line in interval stanza). No improvement!

Apache error log says:

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

May it be that GBrowse does not know about the Bio::DB::BigWig
adapter? I think I first installed GBrowse and then the BigWig module!
May this be the reason?

Maxim

2010/6/10 Lincoln Stein <[hidden email]>:

> Hi,
> This should work. I second the opinion that it is likely a permissions issue
> for the web server. Do you see any error messages in the server error log?
> Lincoln
>
> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>
>> Hi,
>>
>> In order to test whether I was able to overcome my problems to display
>> wiggle data in an appropriate way I decided to test the available
>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>
>> Next I set up a human genome database on my MySQL backend and
>> everything works like a charm.
>>
>> Unfortunately the bigWig data is not showing up, basically there is
>> nothing visible, not even an empty track lane. What I did:
>>
>> I converted a vstep wiggle file using the wigToBigWig application. The
>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>> a Perl-script using the Bio::DB::BigWig module and I was able to
>> extract some data with it.
>>
>> Then I added those lines to my configuration file:
>> [BigWig:database]
>>
>>  db_adaptor    = Bio::DB::BigWig
>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>
>>
>>  [BigWigIntervals]
>>  feature  = summary
>>  database = BigWig
>>  glyph    = wiggle_whiskers
>>  min_score = 0
>>  max_score = 80
>>  key       = test bigWig
>>
>> Does anyone have clue what I might be doing wrong?
>>
>> Maxim
>>
>> P.S: Apache error log says:
>> --------------------- WARNING ---------------------
>> MSG: Got a sequence with no letters in it cannot guess alphabet
>> ---------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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|

Re: how to display bigWig data

Lincoln Stein

Are the chromosome seq_ids identical between the SeqFeature::Store database and the bigwig file?

This one is a very good suggestion; I've been bitten by it myself!
 
Are the stanza titles unique in the conf file?
Are you able to see other tracks, or is it only the bigwig track that won't display?
Are you able to display other data using the xyplot family of adaptors? Say, data stored directly in the SeqFeature::Store database directly, or from the wiggle adaptor?

Tim
--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112



On 6/11/10 9:58 AM, "Lincoln Stein" <[hidden email]> wrote:

That error message is coming from something else, like the GC content track, and not from bigwig.  I really do not understand what is going on. If the bigwig file permissions are wrong, then you should see an error about being unable to open the file. If the adaptor module cannot be found, you should get a very verbose error complaining that the database adaptor is missing.

The installation order shouldn't matter; nor should the "category" option, which simply changes where the track label is displayed in the track table.

Are other people on this list using the BigWig adaptor successfully?

Lincoln

On Fri, Jun 11, 2010 at 5:28 AM, Maxim <[hidden email]> wrote:
Hi,

I changed everything according to the above suggestions (permissions,
extra line in interval stanza). No improvement!

Apache error log says:

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

May it be that GBrowse does not know about the Bio::DB::BigWig
adapter? I think I first installed GBrowse and then the BigWig module!
May this be the reason?

Maxim

2010/6/10 Lincoln Stein <[hidden email]>:
> Hi,
> This should work. I second the opinion that it is likely a permissions issue
> for the web server. Do you see any error messages in the server error log?
> Lincoln
>
> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>
>> Hi,
>>
>> In order to test whether I was able to overcome my problems to display
>> wiggle data in an appropriate way I decided to test the available
>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>
>> Next I set up a human genome database on my MySQL backend and
>> everything works like a charm.
>>
>> Unfortunately the bigWig data is not showing up, basically there is
>> nothing visible, not even an empty track lane. What I did:
>>
>> I converted a vstep wiggle file using the wigToBigWig application. The
>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>> a Perl-script using the Bio::DB::BigWig module and I was able to
>> extract some data with it.
>>
>> Then I added those lines to my configuration file:
>> [BigWig:database]
>>
>>  db_adaptor    = Bio::DB::BigWig
>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>
>>
>>  [BigWigIntervals]
>>  feature  = summary
>>  database = BigWig
>>  glyph    = wiggle_whiskers
>>  min_score = 0
>>  max_score = 80
>>  key       = test bigWig
>>
>> Does anyone have clue what I might be doing wrong?
>>
>> Maxim
>>
>> P.S: Apache error log says:
>> --------------------- WARNING ---------------------
>> MSG: Got a sequence with no letters in it cannot guess alphabet
>> ---------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>





--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: how to display bigWig data

Maxim-4
In reply to this post by Timothy Parnell
Hi,

sorry, took me some time to setup the wiggle/Seqfeature data:

This part does work, and actually I'm really impressed, as this is the
first time that the data looks like expected, must be due to upgrading
to latest GBrowse, Bio:Graphics modules. So the wiggle:xyplot is not
the problem. I still do not like the fact that the data takes about
3Gb, the corresponding BigWig is only 200Mb. Therefore I'm still very
interested to get the BigWig part running.

Anyhow there is now a strange problem after I have modified the
configuration file. I don't know what is different know, but as soon
as I add the bigwig part, I get 500 internal server error message.

Apache says:
gbrowse going down... at /usr/local/apache/cgi-bin/gb2/gbrowse line 41.
Unknown database defined for BigWig:database at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line
747.
[Mon Jun 14 07:56:36 2010] [error] [client 127.0.0.1] Premature end of
script headers: gbrowse, referer:
http://127.0.0.1/gb2/gbrowse/hg18min/?name=chr16%3A$$r16%3A66092277..66292276

What does this statement mean: accessibility of the database (BigWig
file) or general ignorance of this type of adaptor?

Maxim






2010/6/11 Timothy Parnell <[hidden email]>:

> Lincoln,
> Yes, I've been using the BigWig adaptor successfully. I have only used it for a few tracks so far in a development setting, but I've found it to be quite robust over the wiggle adaptor (see an earlier thread of mine). I'm in the process of converting most of my data to this and the SeqFeature::Store database, migrating from the old (...slow...) Bio::DB::GFF databases, so I'll be able to put it through its paces in another week or two.
>
> Maxim,
> Some other questions.
> Are the chromosome seq_ids identical between the SeqFeature::Store database and the bigwig file?
> Are the stanza titles unique in the conf file?
> Are you able to see other tracks, or is it only the bigwig track that won't display?
> Are you able to display other data using the xyplot family of adaptors? Say, data stored directly in the SeqFeature::Store database directly, or from the wiggle adaptor?
>
> Tim
> --
>
> Timothy J Parnell, PhD.
> Research Associate
> Howard Hughes Medical Institute
> Department of Oncology
> Huntsman Cancer Institute
> University of Utah
> Salt Lake City, UT 84112
>
>
>
> On 6/11/10 9:58 AM, "Lincoln Stein" <[hidden email]> wrote:
>
> That error message is coming from something else, like the GC content track, and not from bigwig.  I really do not understand what is going on. If the bigwig file permissions are wrong, then you should see an error about being unable to open the file. If the adaptor module cannot be found, you should get a very verbose error complaining that the database adaptor is missing.
>
> The installation order shouldn't matter; nor should the "category" option, which simply changes where the track label is displayed in the track table.
>
> Are other people on this list using the BigWig adaptor successfully?
>
> Lincoln
>
> On Fri, Jun 11, 2010 at 5:28 AM, Maxim <[hidden email]> wrote:
> Hi,
>
> I changed everything according to the above suggestions (permissions,
> extra line in interval stanza). No improvement!
>
> Apache error log says:
>
> --------------------- WARNING ---------------------
> MSG: Got a sequence with no letters in it cannot guess alphabet
> ---------------------------------------------------
>
> May it be that GBrowse does not know about the Bio::DB::BigWig
> adapter? I think I first installed GBrowse and then the BigWig module!
> May this be the reason?
>
> Maxim
>
> 2010/6/10 Lincoln Stein <[hidden email]>:
>> Hi,
>> This should work. I second the opinion that it is likely a permissions issue
>> for the web server. Do you see any error messages in the server error log?
>> Lincoln
>>
>> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> In order to test whether I was able to overcome my problems to display
>>> wiggle data in an appropriate way I decided to test the available
>>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>>
>>> Next I set up a human genome database on my MySQL backend and
>>> everything works like a charm.
>>>
>>> Unfortunately the bigWig data is not showing up, basically there is
>>> nothing visible, not even an empty track lane. What I did:
>>>
>>> I converted a vstep wiggle file using the wigToBigWig application. The
>>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>>> a Perl-script using the Bio::DB::BigWig module and I was able to
>>> extract some data with it.
>>>
>>> Then I added those lines to my configuration file:
>>> [BigWig:database]
>>>
>>>  db_adaptor    = Bio::DB::BigWig
>>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>>
>>>
>>>  [BigWigIntervals]
>>>  feature  = summary
>>>  database = BigWig
>>>  glyph    = wiggle_whiskers
>>>  min_score = 0
>>>  max_score = 80
>>>  key       = test bigWig
>>>
>>> Does anyone have clue what I might be doing wrong?
>>>
>>> Maxim
>>>
>>> P.S: Apache error log says:
>>> --------------------- WARNING ---------------------
>>> MSG: Got a sequence with no letters in it cannot guess alphabet
>>> ---------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>>
>
>
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: how to display bigWig data

Lincoln Stein

Could you paste in the relevant parts of your configuration file? I would like to see the [XXX:database] stanza that defines the bigwig database and the [track] section that uses this database.

Lincoln

On Mon, Jun 14, 2010 at 11:09 AM, Maxim <[hidden email]> wrote:
Hi,

sorry, took me some time to setup the wiggle/Seqfeature data:

This part does work, and actually I'm really impressed, as this is the
first time that the data looks like expected, must be due to upgrading
to latest GBrowse, Bio:Graphics modules. So the wiggle:xyplot is not
the problem. I still do not like the fact that the data takes about
3Gb, the corresponding BigWig is only 200Mb. Therefore I'm still very
interested to get the BigWig part running.

Anyhow there is now a strange problem after I have modified the
configuration file. I don't know what is different know, but as soon
as I add the bigwig part, I get 500 internal server error message.

Apache says:
gbrowse going down... at /usr/local/apache/cgi-bin/gb2/gbrowse line 41.
Unknown database defined for BigWig:database at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line
747.
[Mon Jun 14 07:56:36 2010] [error] [client 127.0.0.1] Premature end of
script headers: gbrowse, referer:
http://127.0.0.1/gb2/gbrowse/hg18min/?name=chr16%3A$$r16%3A66092277..66292276

What does this statement mean: accessibility of the database (BigWig
file) or general ignorance of this type of adaptor?

Maxim






2010/6/11 Timothy Parnell <[hidden email]>:
> Lincoln,
> Yes, I've been using the BigWig adaptor successfully. I have only used it for a few tracks so far in a development setting, but I've found it to be quite robust over the wiggle adaptor (see an earlier thread of mine). I'm in the process of converting most of my data to this and the SeqFeature::Store database, migrating from the old (...slow...) Bio::DB::GFF databases, so I'll be able to put it through its paces in another week or two.
>
> Maxim,
> Some other questions.
> Are the chromosome seq_ids identical between the SeqFeature::Store database and the bigwig file?
> Are the stanza titles unique in the conf file?
> Are you able to see other tracks, or is it only the bigwig track that won't display?
> Are you able to display other data using the xyplot family of adaptors? Say, data stored directly in the SeqFeature::Store database directly, or from the wiggle adaptor?
>
> Tim
> --
>
> Timothy J Parnell, PhD.
> Research Associate
> Howard Hughes Medical Institute
> Department of Oncology
> Huntsman Cancer Institute
> University of Utah
> Salt Lake City, UT 84112
>
>
>
> On 6/11/10 9:58 AM, "Lincoln Stein" <[hidden email]> wrote:
>
> That error message is coming from something else, like the GC content track, and not from bigwig.  I really do not understand what is going on. If the bigwig file permissions are wrong, then you should see an error about being unable to open the file. If the adaptor module cannot be found, you should get a very verbose error complaining that the database adaptor is missing.
>
> The installation order shouldn't matter; nor should the "category" option, which simply changes where the track label is displayed in the track table.
>
> Are other people on this list using the BigWig adaptor successfully?
>
> Lincoln
>
> On Fri, Jun 11, 2010 at 5:28 AM, Maxim <[hidden email]> wrote:
> Hi,
>
> I changed everything according to the above suggestions (permissions,
> extra line in interval stanza). No improvement!
>
> Apache error log says:
>
> --------------------- WARNING ---------------------
> MSG: Got a sequence with no letters in it cannot guess alphabet
> ---------------------------------------------------
>
> May it be that GBrowse does not know about the Bio::DB::BigWig
> adapter? I think I first installed GBrowse and then the BigWig module!
> May this be the reason?
>
> Maxim
>
> 2010/6/10 Lincoln Stein <[hidden email]>:
>> Hi,
>> This should work. I second the opinion that it is likely a permissions issue
>> for the web server. Do you see any error messages in the server error log?
>> Lincoln
>>
>> On Thu, Jun 10, 2010 at 11:06 AM, Maxim <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> In order to test whether I was able to overcome my problems to display
>>> wiggle data in an appropriate way I decided to test the available
>>> bigWig adapter. I did a fresh install of Gbrowse 2.08 , BioGraphics
>>> 2.09 , Jim Kent's source tree and  Bio-BigFile 1.03.
>>>
>>> Next I set up a human genome database on my MySQL backend and
>>> everything works like a charm.
>>>
>>> Unfortunately the bigWig data is not showing up, basically there is
>>> nothing visible, not even an empty track lane. What I did:
>>>
>>> I converted a vstep wiggle file using the wigToBigWig application. The
>>> file is ok as I can use it on UCSC Browser, additonally I tested it in
>>> a Perl-script using the Bio::DB::BigWig module and I was able to
>>> extract some data with it.
>>>
>>> Then I added those lines to my configuration file:
>>> [BigWig:database]
>>>
>>>  db_adaptor    = Bio::DB::BigWig
>>>  db_args       = -bigwig /home/gbrowse/BigWig/test.bigWig
>>>
>>>
>>>  [BigWigIntervals]
>>>  feature  = summary
>>>  database = BigWig
>>>  glyph    = wiggle_whiskers
>>>  min_score = 0
>>>  max_score = 80
>>>  key       = test bigWig
>>>
>>> Does anyone have clue what I might be doing wrong?
>>>
>>> Maxim
>>>
>>> P.S: Apache error log says:
>>> --------------------- WARNING ---------------------
>>> MSG: Got a sequence with no letters in it cannot guess alphabet
>>> ---------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>>
>
>
>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse