[Gmod-ajax] XYPlot autoscale doesn't work with flatfile-to-json

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[Gmod-ajax] XYPlot autoscale doesn't work with flatfile-to-json

Gwendoline Andres
Hello,

I want to use "autoscale" : "local", with a
JBrowse/View/Track/Wiggle/XYPlot track; but it does not work (with the
1.11.1 version or earlier).
I am using flatfile-to-json to build data :
bin/flatfile-to-json.pl --gff data/mydata.gff --trackLabel tiling_exp
--out real_data/json/test --trackType JBrowse/View/Track/Wiggle/XYPlot
--key 'Tiling experiment'

Even if "local" is the default value, I try adding "autoscale" : "local"
in track configuration in trackList.json but it doesn't resolve the
problem (there is no max_score and min_score defined).

Is it a known issue?

Regards,

--
Gwendoline Andres
Service Informatique et Bio-informatique (SIB)
Embrc-France JDA3
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46


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Re: XYPlot autoscale doesn't work with flatfile-to-json

Robert Buels-2
I don't think it's a known issue.

Would you be able to send me a sample of the reference sequence and data
that you're working with, so I can isolate the problem?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/22/2014 05:42 AM, Gwendoline Andres wrote:

> Hello,
>
> I want to use "autoscale" : "local", with a
> JBrowse/View/Track/Wiggle/XYPlot track; but it does not work (with the
> 1.11.1 version or earlier).
> I am using flatfile-to-json to build data :
> bin/flatfile-to-json.pl --gff data/mydata.gff --trackLabel tiling_exp
> --out real_data/json/test --trackType JBrowse/View/Track/Wiggle/XYPlot
> --key 'Tiling experiment'
>
> Even if "local" is the default value, I try adding "autoscale" : "local"
> in track configuration in trackList.json but it doesn't resolve the
> problem (there is no max_score and min_score defined).
>
> Is it a known issue?
>
> Regards,
>

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Re: XYPlot autoscale doesn't work with flatfile-to-json

Robert Buels-2
Adding the mailing list back in.

Ah, OK I see what is going on.  Yes, NCList stores (which is what
flatfile-to-json makes) don't keep stats on the `score` attributes of
features, so the Wiggle/XYPlot and Wiggle/Density tracks can't do
autoscaling.

If you must have autoscaling, probably the best thing to do would be to
convert your GFF to BedGraph (could do this with just a little perl
one-liner) and from there to a BigWig file (using bedGraphToBigWig from
the UCSC kent sources).

Does that help?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/27/2014 05:52 AM, Gwendoline Andres wrote:

> Hello,
>
> Even with a good gff3 it is not working.
>
> Here are my command lines (with JBrowse-1.11.1):
> bin/prepare-refseqs.pl --fasta data/ecto_sctg_0.fa --out real_data/test
> bin/flatfile-to-json.pl --gff data/tiling2.gff --trackLabel tilling_test
> --out real_data/test/ --trackType JBrowse/View/Track/Wiggle/XYPlot --key
> 'Tiling experiment test'
>
> Sorry I don't know if I am allowed to send my data to the mailling list
> that why I just send it to you.
>
> Regards,
>
> Gwendoline
>
> Le 22/01/2014 18:34, Gwendoline Andres a écrit :
>> Preparing my sample I notice that I add a too many tabulations in my
>> gff file (one more after the 9th column), I think it may be the problem.
>> I will do more tests and re-write to the mailing list after.
>>
>> Thank you very much for asking me a sample!
>>
>> Gwendoline
>>
>> Le 22/01/2014 17:27, Robert Buels a écrit :
>>> I don't think it's a known issue.
>>>
>>> Would you be able to send me a sample of the reference sequence and
>>> data that you're working with, so I can isolate the problem?
>>>
>>>
>>> Robert Buels
>>> Lead Developer
>>> JBrowse - http://jbrowse.org
>>>
>>> On 01/22/2014 05:42 AM, Gwendoline Andres wrote:
>>>> Hello,
>>>>
>>>> I want to use "autoscale" : "local", with a
>>>> JBrowse/View/Track/Wiggle/XYPlot track; but it does not work (with the
>>>> 1.11.1 version or earlier).
>>>> I am using flatfile-to-json to build data :
>>>> bin/flatfile-to-json.pl --gff data/mydata.gff --trackLabel tiling_exp
>>>> --out real_data/json/test --trackType JBrowse/View/Track/Wiggle/XYPlot
>>>> --key 'Tiling experiment'
>>>>
>>>> Even if "local" is the default value, I try adding "autoscale" :
>>>> "local"
>>>> in track configuration in trackList.json but it doesn't resolve the
>>>> problem (there is no max_score and min_score defined).
>>>>
>>>> Is it a known issue?
>>>>
>>>> Regards,
>>>>
>>
>

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Re: XYPlot autoscale doesn't work with flatfile-to-json

Gwendoline Andres
Ok thank you very much for your answer.
I will do that

Regards,
Gwendoline


Le 06/02/2014 06:10, Robert Buels a écrit :

> Adding the mailing list back in.
>
> Ah, OK I see what is going on.  Yes, NCList stores (which is what
> flatfile-to-json makes) don't keep stats on the `score` attributes of
> features, so the Wiggle/XYPlot and Wiggle/Density tracks can't do
> autoscaling.
>
> If you must have autoscaling, probably the best thing to do would be
> to convert your GFF to BedGraph (could do this with just a little perl
> one-liner) and from there to a BigWig file (using bedGraphToBigWig
> from the UCSC kent sources).
>
> Does that help?
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 01/27/2014 05:52 AM, Gwendoline Andres wrote:
>> Hello,
>>
>> Even with a good gff3 it is not working.
>>
>> Here are my command lines (with JBrowse-1.11.1):
>> bin/prepare-refseqs.pl --fasta data/ecto_sctg_0.fa --out real_data/test
>> bin/flatfile-to-json.pl --gff data/tiling2.gff --trackLabel tilling_test
>> --out real_data/test/ --trackType JBrowse/View/Track/Wiggle/XYPlot --key
>> 'Tiling experiment test'
>>
>> Sorry I don't know if I am allowed to send my data to the mailling list
>> that why I just send it to you.
>>
>> Regards,
>>
>> Gwendoline
>>
>> Le 22/01/2014 18:34, Gwendoline Andres a écrit :
>>> Preparing my sample I notice that I add a too many tabulations in my
>>> gff file (one more after the 9th column), I think it may be the
>>> problem.
>>> I will do more tests and re-write to the mailing list after.
>>>
>>> Thank you very much for asking me a sample!
>>>
>>> Gwendoline
>>>
>>> Le 22/01/2014 17:27, Robert Buels a écrit :
>>>> I don't think it's a known issue.
>>>>
>>>> Would you be able to send me a sample of the reference sequence and
>>>> data that you're working with, so I can isolate the problem?
>>>>
>>>>
>>>> Robert Buels
>>>> Lead Developer
>>>> JBrowse - http://jbrowse.org
>>>>
>>>> On 01/22/2014 05:42 AM, Gwendoline Andres wrote:
>>>>> Hello,
>>>>>
>>>>> I want to use "autoscale" : "local", with a
>>>>> JBrowse/View/Track/Wiggle/XYPlot track; but it does not work (with
>>>>> the
>>>>> 1.11.1 version or earlier).
>>>>> I am using flatfile-to-json to build data :
>>>>> bin/flatfile-to-json.pl --gff data/mydata.gff --trackLabel tiling_exp
>>>>> --out real_data/json/test --trackType
>>>>> JBrowse/View/Track/Wiggle/XYPlot
>>>>> --key 'Tiling experiment'
>>>>>
>>>>> Even if "local" is the default value, I try adding "autoscale" :
>>>>> "local"
>>>>> in track configuration in trackList.json but it doesn't resolve the
>>>>> problem (there is no max_score and min_score defined).
>>>>>
>>>>> Is it a known issue?
>>>>>
>>>>> Regards,
>>>>>
>>>
>>

--
Gwendoline Andres
Service Informatique et Bio-informatique (SIB)
Embrc-France JDA3
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46


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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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