[Galaxy-user] Chip-chip data

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[Galaxy-user] Chip-chip data

Laura Elnitski
Hi-

the chip-chip data is in wiggle format and galaxy sends this message 
 error, format: wig, database: hg17
Info: --------------------------------------------------------------------------- Reached output limit of 100000 data values, please make region smaller, or set a higher output line limit with the filter settings. --------------------------------------------------------------------------- 

A search for only chr 7 produces the same  error as the whole genome search. Is there any way to do a minimum of one chromosome at a time?

Thanks very much,
Laura

Laura Elnitski, Ph.D.

Head Genomic Functional Analysis Section

Genome Technology Branch

National Human Genome Research Institute

National Institutes of Health

5625 Fishers Lane, Rm. 5N-01R

Rockville, MD 20852

phone: 301-451-0265

fax: 301-435-6170



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Re: Chip-chip data

James Taylor
Laura,

That message is actually from the table browser. If you select "filter"  
on the table browser output page you can increase this limit to  
10,000,000 rows (wiggle format has one line per data point, so any  
given chromosome or even encode region will likely have more than  
100,000 lines).

-- jt

On Mar 30, 2006, at 5:57 PM, Laura Elnitski wrote:

> Hi-
>
> the chip-chip data is in wiggle format and galaxy sends this message 
>  error, format: wig, database: hg17
> Info:  
> -----------------------------------------------------------------------
> ---- Reached output limit of 100000 data values, please make region  
> smaller, or set a higher output line limit with the filter settings.  
> -----------------------------------------------------------------------
> ---- 
>
> A search for only chr 7 produces the same  error as the whole genome  
> search. Is there any way to do a minimum of one chromosome at a time?
>
> Thanks very much,
> Laura
>
> Laura Elnitski, Ph.D.
> Head Genomic Functional Analysis Section
> Genome Technology Branch
> National Human Genome Research Institute
> National Institutes of Health
> 5625 Fishers Lane, Rm. 5N-01R
> Rockville, MD 20852
> phone: 301-451-0265
> fax: 301-435-6170
>
>
>
> _______________________________________________
> Galaxy-user mailing list
> [hidden email]
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user


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Re: Chip-chip data

Laura Elnitski
Oh- of course--- I was thinking the message was from Galaxy and the use of the filter option in that context wasn't clear to me.

Thanks very much!

Laura
On Mar 30, 2006, at 6:22 PM, James Taylor wrote:

Laura,

That message is actually from the table browser. If you select "filter" 
on the table browser output page you can increase this limit to 
10,000,000 rows (wiggle format has one line per data point, so any 
given chromosome or even encode region will likely have more than 
100,000 lines).

-- jt

On Mar 30, 2006, at 5:57 PM, Laura Elnitski wrote:

> Hi-
>
> the chip-chip data is in wiggle format and galaxy sends this message 
>  error, format: wig, database: hg17
> Info: 
> -----------------------------------------------------------------------
> ---- Reached output limit of 100000 data values, please make region 
> smaller, or set a higher output line limit with the filter settings. 
> -----------------------------------------------------------------------
> ---- 
>
> A search for only chr 7 produces the same  error as the whole genome 
> search. Is there any way to do a minimum of one chromosome at a time?
>
> Thanks very much,
> Laura
>
> Laura Elnitski, Ph.D.
> Head Genomic Functional Analysis Section
> Genome Technology Branch
> National Human Genome Research Institute
> National Institutes of Health
> 5625 Fishers Lane, Rm. 5N-01R
> Rockville, MD 20852
> phone: 301-451-0265
> fax: 301-435-6170
>
>
>
> _______________________________________________
> Galaxy-user mailing list
> [hidden email]
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user


Laura Elnitski, Ph.D.

Head Genomic Functional Analysis Section

Genome Technology Branch

National Human Genome Research Institute

National Institutes of Health

5625 Fishers Lane, Rm. 5N-01R

Rockville, MD 20852

phone: 301-451-0265

fax: 301-435-6170