Jen,
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?
Mike
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
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
email: mlsi...@ncsu.edu
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