track type=wiggle_0 visibility=full name="Smc3_mES" autoScale=on color=100,0,100	1
track visibility=dense name="Smc3_mES enriched regions - 1e-09"  color=100,0,100	892178

On Apr 16, 2012, at 10:35 AM, Jennifer Jackson wrote:

Hi Mike,

I apologize if I wasn't clear, but the 'Select' was to show you how to identify the multi-track group wig files. I wanted to give you a way to screen similar files going forward.

The wig-to-bigWig program in Galaxy comes from UCSC. It accepts .wig files with a single track group as input:
http://genome.ucsc.edu/goldenPath/help/bigWig.html (see step #1)

The data author lab can either submit the data as single track group .wig files, or, if you are confident that the multiple track group .wig format is expected and OK from this source, split the file. There are no specific tools in Galaxy to do this, but something like this would work:

- Text Manipulation -> "Add column", "1", Iterate? = yes
- "Select", "track"
- note the line number of track lines
- "Remove beginning of a file", using line numbers, and the -original- .wig file, to break up into individual .wig files.

Good luck!

Jen
Galaxy team

On 4/16/12 6:57 AM, Michael Sikes wrote:

Jennifer,

Thanks for your help. I ran the filter and sort tool as advised, and

then ran the wig to bigwig on the new history item generated by the

filter. This time I got a different error:

84: Wig-to-bigWig on data 83 <https://main.g2.bx.psu.edu/history>

0 bytes

An error occurred running this job:/stdin is empty of data

Error running wigToBigWig.

/

<https://main.g2.bx.psu.edu/dataset/errors?id=6818347><https://main.g2.bx.psu.edu/datasets/0f70746579b165e2/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6818347>

<https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display/?preview=True><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/edit><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/delete?show_deleted_on_refresh=False>

83: Select on data 49 <https://main.g2.bx.psu.edu/history>

1 line, 1 comments

format: wig, database: mm8

Info: Matching pattern: track

<https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display?to_ext=wig><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6818275><https://main.g2.bx.psu.edu/history>

<https://main.g2.bx.psu.edu/tag/retag?item_id=b4fb2e8c767b4258&item_class=HistoryDatasetAssociation><https://main.g2.bx.psu.edu/dataset/annotate?id=b4fb2e8c767b4258>

Again, I'm sure I left off something obvious. Could you tell me what I

did wrong?

Thanks,

Mike

On Apr 13, 2012, at 1:27 PM, Jennifer Jackson wrote:

Hi Michael,

This particular .wig file has a data format problem that is the root

cause of the conversion error. Specifically, there is an extra track

line in the file. This can be found using unix tools with a grep or in

Galaxy with the tool "Filter and Sort -> Select" by matching the

pattern "track".

Ideally this would be corrected and resubmitted by the data author

before use, since how/why this was inserted and what impact it has

would need to be examined.

Since you noticed problems with other GEO files (conversion problems),

verifying the .wig format and making any necessary corrections would

also be advised.

Hopefully this helps!

Best,

Jen

Galaxy team