A couple of uninformed questions. I gather from your response that the author lab submitted a multiple track group .wig file instead of a single track group .wig file, and that I need to generate a single track group file before the bigwig conversion will work. So, with regard to the instructions below, I am to run the text manipulation on the original author submitted .wig file. Then run "filter and sort-- Select lines that match an expression" on the newly created file that: "Matching" the pattern: "track". This generates yet another file that has the following info:
88: Select on data 87
1 line, 1 comments
format: wig, database: mm8
Info: Matching pattern: track

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 Is the number 892173 the number of track lines? If so, do I then do the "Remove beginning of a file" using 892178 on the original author .wig file?

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: (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!

Galaxy team

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

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 <>
0 bytes
An error occurred running this job:/stdin is empty of data
Error running wigToBigWig.
<>< ><> < ><>< >
83: Select on data 49 <>
1 line, 1 comments
format: wig, database: mm8
Info: Matching pattern: track
< >< show_params>< id=6818275><> < ><>

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


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!


Galaxy team

Michael Sikes, Ph.D.
Associate Professor of Immunology
North Carolina State University
Microbiology Department
4524A Gardner Hall
Campus Box 7615
Raleigh, NC 27695
Ph: 919-513-0528
Fax: 919-515-7867

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