sequence quality values

classic Classic list List threaded Threaded
11 messages Options
Reply | Threaded
Open this post in threaded view
|

sequence quality values

Lukas A. Mueller
Hi,

how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)

cheers
Lukas


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Scott Cain
Hi Lukas,

Given that there's currently no place for them, I'd say it's a featureprop :-)

Scott


On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:

> Hi,
>
> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>
> cheers
> Lukas
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

David Emmert
In reply to this post by Lukas A. Mueller
Hi Lukas,

I'm curious.  What does the quality values data look like?  
Is it continuous data, or ???

-Dave

>From [hidden email]  Thu Oct 28 10:16:43 2010
>> To: Lukas Mueller <[hidden email]>
>> Cc: gmod schema <[hidden email]>
>> Subject: Re: [Gmod-schema] sequence quality values
>>
>> Hi Lukas,
>>
>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>> > Hi,
>> >
>> > how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>> >
>> > cheers
>> > Lukas
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> > Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> > http://p.sf.net/sfu/nokia-dev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Lukas A. Mueller
Standard phred quality look like this:

45 65 67 56 67 78 ...

(if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.

cheers
Lukas

On Oct 28, 2010, at 10:25 AM, David Emmert wrote:

> Hi Lukas,
>
> I'm curious.  What does the quality values data look like?  
> Is it continuous data, or ???
>
> -Dave
>
> From [hidden email]  Thu Oct 28 10:16:43 2010
>>> To: Lukas Mueller <[hidden email]>
>>> Cc: gmod schema <[hidden email]>
>>> Subject: Re: [Gmod-schema] sequence quality values
>>>
>>> Hi Lukas,
>>>
>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>>>> Hi,
>>>>
>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>>>>
>>>> cheers
>>>> Lukas
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

David Emmert
In reply to this post by Lukas A. Mueller

What do you expect to be doing with the phred scores for particular
regions?  Will you need to be computing on them frequently, for
instance?

-D

>From [hidden email]  Thu Oct 28 10:35:34 2010
>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>> To: David Emmert <[hidden email]>
>> Cc: "[hidden email]" <[hidden email]>
>> Subject: Re: [Gmod-schema] sequence quality values
>>
>> Standard phred quality look like this:
>>
>> 45 65 67 56 67 78 ...
>>
>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>
>> cheers
>> Lukas
>>
>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>>
>> > Hi Lukas,
>> >
>> > I'm curious.  What does the quality values data look like?  
>> > Is it continuous data, or ???
>> >
>> > -Dave
>> >
>> > From [hidden email]  Thu Oct 28 10:16:43 2010
>> >>> To: Lukas Mueller <[hidden email]>
>> >>> Cc: gmod schema <[hidden email]>
>> >>> Subject: Re: [Gmod-schema] sequence quality values
>> >>>
>> >>> Hi Lukas,
>> >>>
>> >>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>> >>>
>> >>> Scott
>> >>>
>> >>>
>> >>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>> >>>> Hi,
>> >>>>
>> >>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>> >>>>
>> >>>> cheers
>> >>>> Lukas
>> >>>>
>> >>>>
>> >>>> ------------------------------------------------------------------------------
>> >>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>> _______________________________________________
>> >>>> Gmod-schema mailing list
>> >>>> [hidden email]
>> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> ------------------------------------------------------------------------
>> >>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> >>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>> Ontario Institute for Cancer Research
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>> http://p.sf.net/sfu/nokia-dev2dev
>> >>> _______________________________________________
>> >>> Gmod-schema mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>
>> >>>
>>
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Lukas A. Mueller
Hi David,

we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.

cheers
Lukas

On Oct 28, 2010, at 10:51 AM, David Emmert wrote:

>
> What do you expect to be doing with the phred scores for particular
> regions?  Will you need to be computing on them frequently, for
> instance?
>
> -D
>
> From [hidden email]  Thu Oct 28 10:35:34 2010
>>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>>> To: David Emmert <[hidden email]>
>>> Cc: "[hidden email]" <[hidden email]>
>>> Subject: Re: [Gmod-schema] sequence quality values
>>>
>>> Standard phred quality look like this:
>>>
>>> 45 65 67 56 67 78 ...
>>>
>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>>
>>> cheers
>>> Lukas
>>>
>>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>>>
>>>> Hi Lukas,
>>>>
>>>> I'm curious.  What does the quality values data look like?  
>>>> Is it continuous data, or ???
>>>>
>>>> -Dave
>>>>
>>>> From [hidden email]  Thu Oct 28 10:16:43 2010
>>>>>> To: Lukas Mueller <[hidden email]>
>>>>>> Cc: gmod schema <[hidden email]>
>>>>>> Subject: Re: [Gmod-schema] sequence quality values
>>>>>>
>>>>>> Hi Lukas,
>>>>>>
>>>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>>>>>>>
>>>>>>> cheers
>>>>>>> Lukas
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Lukas A. Mueller
In reply to this post by David Emmert
an alternative to listing the space separated qual values would be to use the fastq method for storing that information, which essentially represents each qual value by its ASCII code (+32 I think to exclude the control characters). Then each qual value is one byte.
cheers
Lukas

On Oct 28, 2010, at 10:51 AM, David Emmert wrote:

>
> What do you expect to be doing with the phred scores for particular
> regions?  Will you need to be computing on them frequently, for
> instance?
>
> -D
>
> From [hidden email]  Thu Oct 28 10:35:34 2010
>>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>>> To: David Emmert <[hidden email]>
>>> Cc: "[hidden email]" <[hidden email]>
>>> Subject: Re: [Gmod-schema] sequence quality values
>>>
>>> Standard phred quality look like this:
>>>
>>> 45 65 67 56 67 78 ...
>>>
>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>>
>>> cheers
>>> Lukas
>>>
>>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>>>
>>>> Hi Lukas,
>>>>
>>>> I'm curious.  What does the quality values data look like?  
>>>> Is it continuous data, or ???
>>>>
>>>> -Dave
>>>>
>>>> From [hidden email]  Thu Oct 28 10:16:43 2010
>>>>>> To: Lukas Mueller <[hidden email]>
>>>>>> Cc: gmod schema <[hidden email]>
>>>>>> Subject: Re: [Gmod-schema] sequence quality values
>>>>>>
>>>>>> Hi Lukas,
>>>>>>
>>>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>>>>>>>
>>>>>>> cheers
>>>>>>> Lukas
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Fields, Christopher J
In reply to this post by Lukas A. Mueller
You could also encode those into a FASTQ quality string to condense them down if needed, but I would standardize them into the Sanger FASTQ format (please don't pick Illumina/Solexa variations!).  All of the Bio* projects now have parsers that handle that conversion (I re-wrote the BioPerl one from scratch).

http://www.bioperl.org/wiki/FASTQ_sequence_format

chris

On Oct 28, 2010, at 9:34 AM, Lukas Mueller wrote:

> Standard phred quality look like this:
>
> 45 65 67 56 67 78 ...
>
> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>
> cheers
> Lukas
>
> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>
>> Hi Lukas,
>>
>> I'm curious.  What does the quality values data look like?  
>> Is it continuous data, or ???
>>
>> -Dave
>>
>> From [hidden email]  Thu Oct 28 10:16:43 2010
>>>> To: Lukas Mueller <[hidden email]>
>>>> Cc: gmod schema <[hidden email]>
>>>> Subject: Re: [Gmod-schema] sequence quality values
>>>>
>>>> Hi Lukas,
>>>>
>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>>>>> Hi,
>>>>>
>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>>>>>
>>>>> cheers
>>>>> Lukas
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

David Emmert
In reply to this post by Lukas A. Mueller
Hi Lukas,

I'll preface my suggestion by noting that I found a years-old thread from
Sam Angiuoli when he was at JCVI saying they were making features of type
"consensus_quality_value" (which I don't think was legit SO) for storing
the phred scores, which they were stashing in feature.residues.  Sam
himself admitted that it wasn't pretty, and it certainly isn't, but
you might consider contacting Sam and asking how it worked out in the
long-run.

I think I'd suggest a tweak on Sam's method:  how about making a feature
of one of the "*_draft" SO types (eg, "standard_draft", "high_quality_draft",
etc), corresponding to each region where you have phred scores, then use
a featureloc to associate the "_draft" feature to the region you have
scores for, and stash the actual phred scores in featureloc.residue_info.  

(I may be wrong about the SO type to use - it would probably be a good idea
to ask the SO mavens what they suggest.)

Without going whole hog and implementing a record for each residue score
(which I wouldn't dare, but if you want to, I'd love to discuss how you
might do it), I think this might be your best bet.  You'll still have
to grab & parse the phred scores when analyzing alignments, but at least
you'll have them organized and easy to get to, and - sorry Sam! - not
too horribly ugly an implementation.

But maybe someone will have a better idea...?

Best,

-D

PS: In case you're wondering, my interest in this is because I've been working
with RNA-Seq coverage data, which presents a similar problem of storing
continuous data....

>From [hidden email]  Thu Oct 28 11:02:53 2010
>> Subject: Re: [Gmod-schema] sequence quality values
>> Cc: "[hidden email]" <[hidden email]>
>> To: David Emmert <[hidden email]>
>>
>> Hi David,
>>
>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>>
>> cheers
>> Lukas
>>
>> On Oct 28, 2010, at 10:51 AM, David Emmert wrote:
>>
>> >
>> > What do you expect to be doing with the phred scores for particular
>> > regions?  Will you need to be computing on them frequently, for
>> > instance?
>> >
>> > -D
>> >
>> > From [hidden email]  Thu Oct 28 10:35:34 2010
>> >>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>> >>> To: David Emmert <[hidden email]>
>> >>> Cc: "[hidden email]" <[hidden email]>
>> >>> Subject: Re: [Gmod-schema] sequence quality values
>> >>>
>> >>> Standard phred quality look like this:
>> >>>
>> >>> 45 65 67 56 67 78 ...
>> >>>
>> >>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> >>>
>> >>> cheers
>> >>> Lukas
>> >>>
>> >>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>> >>>
>> >>>> Hi Lukas,
>> >>>>
>> >>>> I'm curious.  What does the quality values data look like?  
>> >>>> Is it continuous data, or ???
>> >>>>
>> >>>> -Dave
>> >>>>
>> >>>> From [hidden email]  Thu Oct 28 10:16:43 2010
>> >>>>>> To: Lukas Mueller <[hidden email]>
>> >>>>>> Cc: gmod schema <[hidden email]>
>> >>>>>> Subject: Re: [Gmod-schema] sequence quality values
>> >>>>>>
>> >>>>>> Hi Lukas,
>> >>>>>>
>> >>>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>> >>>>>>
>> >>>>>> Scott
>> >>>>>>
>> >>>>>>
>> >>>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>> >>>>>>> Hi,
>> >>>>>>>
>> >>>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>> >>>>>>>
>> >>>>>>> cheers
>> >>>>>>> Lukas
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> ------------------------------------------------------------------------------
>> >>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>>>>> _______________________________________________
>> >>>>>>> Gmod-schema mailing list
>> >>>>>>> [hidden email]
>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> --
>> >>>>>> ------------------------------------------------------------------------
>> >>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> >>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>>>>> Ontario Institute for Cancer Research
>> >>>>>>
>> >>>>>> ------------------------------------------------------------------------------
>> >>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>>>> _______________________________________________
>> >>>>>> Gmod-schema mailing list
>> >>>>>> [hidden email]
>> >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>>
>> >>>>>>
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>> http://p.sf.net/sfu/nokia-dev2dev
>> >>> _______________________________________________
>> >>> Gmod-schema mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>
>> >>>
>>
>>
>>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

Lukas A. Mueller
Hi David,

since the quality values are an important and a one-to-one property of the sequence, I was wondering if the easiest wouldn't be to just have an extra field in the table like 'qual' in addition to residues? It could be NULL.

cheers
Lukas

On Oct 28, 2010, at 11:40 AM, David Emmert wrote:

> Hi Lukas,
>
> I'll preface my suggestion by noting that I found a years-old thread from
> Sam Angiuoli when he was at JCVI saying they were making features of type
> "consensus_quality_value" (which I don't think was legit SO) for storing
> the phred scores, which they were stashing in feature.residues.  Sam
> himself admitted that it wasn't pretty, and it certainly isn't, but
> you might consider contacting Sam and asking how it worked out in the
> long-run.
>
> I think I'd suggest a tweak on Sam's method:  how about making a feature
> of one of the "*_draft" SO types (eg, "standard_draft", "high_quality_draft",
> etc), corresponding to each region where you have phred scores, then use
> a featureloc to associate the "_draft" feature to the region you have
> scores for, and stash the actual phred scores in featureloc.residue_info.  
>
> (I may be wrong about the SO type to use - it would probably be a good idea
> to ask the SO mavens what they suggest.)
>
> Without going whole hog and implementing a record for each residue score
> (which I wouldn't dare, but if you want to, I'd love to discuss how you
> might do it), I think this might be your best bet.  You'll still have
> to grab & parse the phred scores when analyzing alignments, but at least
> you'll have them organized and easy to get to, and - sorry Sam! - not
> too horribly ugly an implementation.
>
> But maybe someone will have a better idea...?
>
> Best,
>
> -D
>
> PS: In case you're wondering, my interest in this is because I've been working
> with RNA-Seq coverage data, which presents a similar problem of storing
> continuous data....
>
> From [hidden email]  Thu Oct 28 11:02:53 2010
>>> Subject: Re: [Gmod-schema] sequence quality values
>>> Cc: "[hidden email]" <[hidden email]>
>>> To: David Emmert <[hidden email]>
>>>
>>> Hi David,
>>>
>>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>>>
>>> cheers
>>> Lukas
>>>
>>> On Oct 28, 2010, at 10:51 AM, David Emmert wrote:
>>>
>>>>
>>>> What do you expect to be doing with the phred scores for particular
>>>> regions?  Will you need to be computing on them frequently, for
>>>> instance?
>>>>
>>>> -D
>>>>
>>>> From [hidden email]  Thu Oct 28 10:35:34 2010
>>>>>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>>>>>> To: David Emmert <[hidden email]>
>>>>>> Cc: "[hidden email]" <[hidden email]>
>>>>>> Subject: Re: [Gmod-schema] sequence quality values
>>>>>>
>>>>>> Standard phred quality look like this:
>>>>>>
>>>>>> 45 65 67 56 67 78 ...
>>>>>>
>>>>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>>>>>>
>>>>>> cheers
>>>>>> Lukas
>>>>>>
>>>>>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>>>>>>
>>>>>>> Hi Lukas,
>>>>>>>
>>>>>>> I'm curious.  What does the quality values data look like?  
>>>>>>> Is it continuous data, or ???
>>>>>>>
>>>>>>> -Dave
>>>>>>>
>>>>>>> From [hidden email]  Thu Oct 28 10:16:43 2010
>>>>>>>>> To: Lukas Mueller <[hidden email]>
>>>>>>>>> Cc: gmod schema <[hidden email]>
>>>>>>>>> Subject: Re: [Gmod-schema] sequence quality values
>>>>>>>>>
>>>>>>>>> Hi Lukas,
>>>>>>>>>
>>>>>>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>>>>>>>>>>
>>>>>>>>>> cheers
>>>>>>>>>> Lukas
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-schema mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-schema mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>>
>>>
>>>
>>>


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: sequence quality values

David Emmert
In reply to this post by Lukas A. Mueller

Hi Lukas,

The problem with adding a field like "feature.qual" is that, sooner or
later, someone's going to want to either store attributes of the quality
score, or store more than one score for a given region.  Also, of course,
it can be a pretty time-consuming undertaking to try to build a
consensus within GMOD for a schema change to a core chado table.

I think I'd recommend going with the feature/featureloc solution.  Its
a flexible solution, and I think it may provide a pattern we can exploit
for other continuous datasets.  

Another thing I like about the feature/featureloc solution is that in
not hard-coding the change into the schema, we keep options open in
case someone rolls up later on with a really clever solution for
storing continuous data.

Best,

-D

>From [hidden email]  Thu Oct 28 11:50:26 2010
>> Date: Thu, 28 Oct 2010 11:50:18 -0400
>> Cc: "[hidden email]" <[hidden email]>,
>>         "[hidden email]" <[hidden email]>
>> To: David Emmert <[hidden email]>
>>
>> Hi David,
>>
>> since the quality values are an important and a one-to-one property of the sequence, I was wondering if the easiest wouldn't be to just have an extra field in the table like 'qual' in addition to residues? It could be NULL.
>>
>> cheers
>> Lukas
>>
>> On Oct 28, 2010, at 11:40 AM, David Emmert wrote:
>>
>> > Hi Lukas,
>> >
>> > I'll preface my suggestion by noting that I found a years-old thread from
>> > Sam Angiuoli when he was at JCVI saying they were making features of type
>> > "consensus_quality_value" (which I don't think was legit SO) for storing
>> > the phred scores, which they were stashing in feature.residues.  Sam
>> > himself admitted that it wasn't pretty, and it certainly isn't, but
>> > you might consider contacting Sam and asking how it worked out in the
>> > long-run.
>> >
>> > I think I'd suggest a tweak on Sam's method:  how about making a feature
>> > of one of the "*_draft" SO types (eg, "standard_draft", "high_quality_draft",
>> > etc), corresponding to each region where you have phred scores, then use
>> > a featureloc to associate the "_draft" feature to the region you have
>> > scores for, and stash the actual phred scores in featureloc.residue_info.  
>> >
>> > (I may be wrong about the SO type to use - it would probably be a good idea
>> > to ask the SO mavens what they suggest.)
>> >
>> > Without going whole hog and implementing a record for each residue score
>> > (which I wouldn't dare, but if you want to, I'd love to discuss how you
>> > might do it), I think this might be your best bet.  You'll still have
>> > to grab & parse the phred scores when analyzing alignments, but at least
>> > you'll have them organized and easy to get to, and - sorry Sam! - not
>> > too horribly ugly an implementation.
>> >
>> > But maybe someone will have a better idea...?
>> >
>> > Best,
>> >
>> > -D
>> >
>> > PS: In case you're wondering, my interest in this is because I've been working
>> > with RNA-Seq coverage data, which presents a similar problem of storing
>> > continuous data....
>> >
>> > From [hidden email]  Thu Oct 28 11:02:53 2010
>> >>> Subject: Re: [Gmod-schema] sequence quality values
>> >>> Cc: "[hidden email]" <[hidden email]>
>> >>> To: David Emmert <[hidden email]>
>> >>>
>> >>> Hi David,
>> >>>
>> >>> we would like them to be accessible in an efficient way. For example, when looking at alignments to a genome, the quality score is important to determine if you have a SNP or a problem with the aligned sequence.
>> >>>
>> >>> cheers
>> >>> Lukas
>> >>>
>> >>> On Oct 28, 2010, at 10:51 AM, David Emmert wrote:
>> >>>
>> >>>>
>> >>>> What do you expect to be doing with the phred scores for particular
>> >>>> regions?  Will you need to be computing on them frequently, for
>> >>>> instance?
>> >>>>
>> >>>> -D
>> >>>>
>> >>>> From [hidden email]  Thu Oct 28 10:35:34 2010
>> >>>>>> Date: Thu, 28 Oct 2010 10:34:55 -0400
>> >>>>>> To: David Emmert <[hidden email]>
>> >>>>>> Cc: "[hidden email]" <[hidden email]>
>> >>>>>> Subject: Re: [Gmod-schema] sequence quality values
>> >>>>>>
>> >>>>>> Standard phred quality look like this:
>> >>>>>>
>> >>>>>> 45 65 67 56 67 78 ...
>> >>>>>>
>> >>>>>> (if you are lucky! - the higher the better). These are scores for each nucleotide, in order, separated by a space, of course they can also be single digit values in there.
>> >>>>>>
>> >>>>>> cheers
>> >>>>>> Lukas
>> >>>>>>
>> >>>>>> On Oct 28, 2010, at 10:25 AM, David Emmert wrote:
>> >>>>>>
>> >>>>>>> Hi Lukas,
>> >>>>>>>
>> >>>>>>> I'm curious.  What does the quality values data look like?  
>> >>>>>>> Is it continuous data, or ???
>> >>>>>>>
>> >>>>>>> -Dave
>> >>>>>>>
>> >>>>>>> From [hidden email]  Thu Oct 28 10:16:43 2010
>> >>>>>>>>> To: Lukas Mueller <[hidden email]>
>> >>>>>>>>> Cc: gmod schema <[hidden email]>
>> >>>>>>>>> Subject: Re: [Gmod-schema] sequence quality values
>> >>>>>>>>>
>> >>>>>>>>> Hi Lukas,
>> >>>>>>>>>
>> >>>>>>>>> Given that there's currently no place for them, I'd say it's a featureprop :-)
>> >>>>>>>>>
>> >>>>>>>>> Scott
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> On Thu, Oct 28, 2010 at 9:49 AM, Lukas Mueller <[hidden email]> wrote:
>> >>>>>>>>>> Hi,
>> >>>>>>>>>>
>> >>>>>>>>>> how do you store quality values for sequences in the feature table? (Don''t tell me it's a feature prop  :-)
>> >>>>>>>>>>
>> >>>>>>>>>> cheers
>> >>>>>>>>>> Lukas
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> ------------------------------------------------------------------------------
>> >>>>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>>>>>>>> _______________________________________________
>> >>>>>>>>>> Gmod-schema mailing list
>> >>>>>>>>>> [hidden email]
>> >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> --
>> >>>>>>>>> ------------------------------------------------------------------------
>> >>>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> >>>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>>>>>>>> Ontario Institute for Cancer Research
>> >>>>>>>>>
>> >>>>>>>>> ------------------------------------------------------------------------------
>> >>>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>>>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>>>>>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>>>>>>> _______________________________________________
>> >>>>>>>>> Gmod-schema mailing list
>> >>>>>>>>> [hidden email]
>> >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> ------------------------------------------------------------------------------
>> >>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> >>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> >>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> >>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> >>>>>> http://p.sf.net/sfu/nokia-dev2dev
>> >>>>>> _______________________________________________
>> >>>>>> Gmod-schema mailing list
>> >>>>>> [hidden email]
>> >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>>
>> >>>>>>
>> >>>
>> >>>
>> >>>
>>
>>
>>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema