SigWin-detector Config-Basic
Created: 2009-10-09 13:37:10
Last updated: 2010-04-23 10:06:58
Download WorkflowDetects significant windows in a sequence.
Input: A space-delimited file with (at least) one column containing the input sequence E= {E1, E2, …, EN}. A two-line header should precede the data. Input file example.<o:p></o:p>
Output:
(1) A file containing the detected significant windows for each label. Each data row represents a stretch of consecutive significant windows. Column 1 gives the window size and columns 2 and 3 give the first and last significant windows in the stretch. Output file example.
(2) An XMGRACE configurations file with information on how to plot the resulting SigWin-map (Use: xmgrace -bat file.agrcmd)
Graphical output: An XMGRACE plot displaying the resulting SigWin-map.
Parameters to set: (see module descriptions)<o:p></o:p>
(1) ColumnReader: file_name, column.
(2) SWMedian: min_window_size, max_window_size, step_size.
(3) FDRThresold: FDR_level, threshold
(4) SigWinSelect: Output_file, threshold:
[Launch in wsvlam]
[movie]
IMPORTANT: to RUN this workflow you need grid credentials which are acceptable by the Distibuted ASCI Supercomputer [DAS3]
- Contact the workflow author to get demo credentials
- to use this workflow for real input data, it is better to try to get approriate grid credentials
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Sounds interesting,
but can you please provide some use case/example of how this workflow could be used?
What do you mean exactly with 'significant window'? Are you referring to the sliding windows method? But what is 'significant' exactly?
Thank you for providing a sample files and the description of all the processors used (I found it very difficult to understand the workflow from the description posted here only, because I didn't know what the various processors do).
However, is the input file correct? I can't find any sequence in it.
It is like this:
#size=26740 ncols=2 descr=hg18-htm
#chrom expression
1 10.0
1 13.0
1 286.0
1 0
...
where is the sequence?
Moreover, with which sequences/parameters have you tested this workflow?
Thanks.. sorry, I made too many questions :)
Hi
Sorry for not reacting before to your questions. Actually I had to forward your
questions to the Sigwin-window developper (I'm just a member of the group
who design the workflow system. Following are the commnets:
Sigwin web page: http://staff.science.uva.nl/~inda/SigWin-detector.html
The sequence is the second column (a sequence here is just a list of numbers ordered somehow). For the temperatures the ordering is in time, for the transcriptome the ordering is position in the chromossome.
Significant windows are the sliding windows for which the median value is statistically significantly higher than expected.
I hope this will help, very soon you should be able to run this workfow from on the demo testbed we are setting up
Thanks for your interest in this work