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Error running bedgraph to bigwig on local galaxy

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Error running bedgraph to bigwig on local galaxy

evan clark
When attempting to generate a bigwig file I receive this error.

hashMustFindVal: 'GL000192.1' not found Fatal error: Matched on Error
Error running wigToBigWig.

I have added the chrom len files for galaxy and update the location path
but an unsure what could be causing this issue.


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Re: Error running bedgraph to bigwig on local galaxy

Devon Ryan
Are you using the chromosome lengths for the correct organism and
source? GL000192.1 is a contig name used by Ensembl and Gencode (but
not UCSC!) for GRCh37 (aka hg19).

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, Nov 23, 2016 at 4:12 PM, evan clark <[hidden email]> wrote:

> When attempting to generate a bigwig file I receive this error.
>
> hashMustFindVal: 'GL000192.1' not found Fatal error: Matched on Error Error
> running wigToBigWig.
>
> I have added the chrom len files for galaxy and update the location path but
> an unsure what could be causing this issue.
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
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Re: Error running bedgraph to bigwig on local galaxy

evan clark
Yes, these alignments were done to ensemble, not UCSC.

---
Regards,
Evan Clark

On November 23, 2016 at 10:38:55 AM EST, Devon Ryan <[hidden email]> wrote:
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Are you using the chromosome lengths for the correct organism and
source? GL000192.1 is a contig name used by Ensembl and Gencode (but
not UCSC!) for GRCh37 (aka hg19).

Devon
--
Devon Ryan, Ph.D.
Email: [hidden email]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, Nov 23, 2016 at 4:12 PM, evan clark wrote:

> When attempting to generate a bigwig file I receive this error.
>
> hashMustFindVal: 'GL000192.1' not found Fatal error: Matched on Error Error
> running wigToBigWig.
>
> I have added the chrom len files for galaxy and update the location path but
> an unsure what could be causing this issue.
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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