Gbrowse_syn - help with mercatoraln_to_synhits.pl

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Gbrowse_syn - help with mercatoraln_to_synhits.pl

Jayaraman, Pushkala

Hello Sheldon,

I had a few queries regarding the mercatoraln_to_synhits.pl script.

We have data from the Mercator pipeline from two years ago. Although we have the data, we do not have the “genomes” and the “map” folders that seems to be required by the mercatoraln_to_synhits.pl script.  The fact is that this pipeline was run by Colin Dewey, the developer for Mercator and this was done two years ago.

Could I get a test dataset so that I may understand how that script works and what we may need in addition to the files we have?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: Gbrowse_syn - help with mercatoraln_to_synhits.pl

Sheldon McKay
Hi Pushkala,

Jason Stajich is the author the the script.  I cced him here.

I used an example data set derived from
http://www.biostat.wisc.edu/~cdewey/fly_CAF1/, from which many
mercator data sets can be obtained.

Off-list, I will send you an link to a temporary download page (the
tarball is too big se send as an email attachment) for a file I have
personally tested and loaded into a gbrowse_syn database.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Tue, Jun 15, 2010 at 7:04 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,
>
> I had a few queries regarding the mercatoraln_to_synhits.pl script.
>
> We have data from the Mercator pipeline from two years ago. Although we have
> the data, we do not have the “genomes” and the “map” folders that seems to
> be required by the mercatoraln_to_synhits.pl script.  The fact is that this
> pipeline was run by Colin Dewey, the developer for Mercator and this was
> done two years ago.
>
> Could I get a test dataset so that I may understand how that script works
> and what we may need in addition to the files we have?
>
>
>
> Thanks,
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>

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Re: Gbrowse_syn - help with mercatoraln_to_synhits.pl

Jason Stajich-4
Hi Pushkala -

The genomes and map are files that are located in the 'alignments'
directory which you would need if you want to do anything with the
mercator output as it provides the linkage of the alignment chunks to
the original sequences.

-jason
Sheldon McKay wrote, On 6/16/10 8:05 AM:

> Hi Pushkala,
>
> Jason Stajich is the author the the script.  I cced him here.
>
> I used an example data set derived from
> http://www.biostat.wisc.edu/~cdewey/fly_CAF1/, from which many
> mercator data sets can be obtained.
>
> Off-list, I will send you an link to a temporary download page (the
> tarball is too big se send as an email attachment) for a file I have
> personally tested and loaded into a gbrowse_syn database.
>
> Sheldon
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: [hidden email]
> Google Voice:  (203) 701-9204
>
>
>
> On Tue, Jun 15, 2010 at 7:04 PM, Jayaraman, Pushkala<[hidden email]>  wrote:
>    
>> Hello Sheldon,
>>
>> I had a few queries regarding the mercatoraln_to_synhits.pl script.
>>
>> We have data from the Mercator pipeline from two years ago. Although we have
>> the data, we do not have the “genomes” and the “map” folders that seems to
>> be required by the mercatoraln_to_synhits.pl script.  The fact is that this
>> pipeline was run by Colin Dewey, the developer for Mercator and this was
>> done two years ago.
>>
>> Could I get a test dataset so that I may understand how that script works
>> and what we may need in addition to the files we have?
>>
>>
>>
>> Thanks,
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>>      

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