BigWig help

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BigWig help

Alper Yilmaz
Hi,

I need some help for BigWig configuration to display as a track.
Although I tried to use the config options from the recent emails
regarding BigWig, I'm just getting an empty track. Apache logs does
not indicate errors related to BigWig.

My config is here: http://pastebin.com/FseE4imz    (I clipped sam/bam
related tracks)

I used wigToBigWig.pl script to convert wig file into .bw format, as
described here: http://pastebin.com/hfVM24Qf

thanks,

Alper Yilmaz
Post-doctoral Researcher
Plant Biotechnology Center
The Ohio State University
1060 Carmack Rd
Columbus, OH 43210
(614)688-4954

------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
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Re: BigWig help

Keiran Raine
Hi Alperm

You appear to be working with a single BW file, try this syntax:


[mariagl15:database]
db_adaptor = Bio::DB::BigWig
db_args    = sub { require Bio::DB::Sam;
                   return (
                       -bigwig => '/var/www/gbrowse2/databases/maize4a53/bigwig/GL15_gl15_pur.bw',
                       );
                 }
search options = none

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 3 Feb 2011, at 23:20, Alper Yilmaz wrote:

Hi,

I need some help for BigWig configuration to display as a track.
Although I tried to use the config options from the recent emails
regarding BigWig, I'm just getting an empty track. Apache logs does
not indicate errors related to BigWig.

My config is here: http://pastebin.com/FseE4imz    (I clipped sam/bam
related tracks)

I used wigToBigWig.pl script to convert wig file into .bw format, as
described here: http://pastebin.com/hfVM24Qf

thanks,

Alper Yilmaz
Post-doctoral Researcher
Plant Biotechnology Center
The Ohio State University
1060 Carmack Rd
Columbus, OH 43210
(614)688-4954

------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
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Re: BigWig help

Timothy Parnell
In reply to this post by Alper Yilmaz
You're using Bio::DB::BigWigSet, which is designed for multiple bw files.
Switch to Bio::DB::BigWig

On 2/3/11 4:20 PM, "Alper Yilmaz" <[hidden email]> wrote:

>Hi,
>
>I need some help for BigWig configuration to display as a track.
>Although I tried to use the config options from the recent emails
>regarding BigWig, I'm just getting an empty track. Apache logs does
>not indicate errors related to BigWig.
>
>My config is here: http://pastebin.com/FseE4imz    (I clipped sam/bam
>related tracks)
>
>I used wigToBigWig.pl script to convert wig file into .bw format, as
>described here: http://pastebin.com/hfVM24Qf
>
>thanks,
>
>Alper Yilmaz
>Post-doctoral Researcher
>Plant Biotechnology Center
>The Ohio State University
>1060 Carmack Rd
>Columbus, OH 43210
>(614)688-4954
>
>--------------------------------------------------------------------------
>----
>The modern datacenter depends on network connectivity to access resources
>and provide services. The best practices for maximizing a physical
>server's
>connectivity to a physical network are well understood - see how these
>rules translate into the virtual world?
>http://p.sf.net/sfu/oracle-sfdevnlfb
>_______________________________________________
>Gmod-gbrowse mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse