Hello, It is difficult to know exactly what the issue may be without knowing more about the setting used with the tool. I can let you know that if the windows are larger in size than the intervals, than the results can be empty without errors (see the " *Note*" on the tool form for details about why). For the example you show, the length of the region is 9 bases, so a window of 9 bases or less would be required for any result from this particular interval. Both BED and Interval format use a "0" based start coordinate, more is in our wiki here: http://wiki.galaxyproject.org/Learn/Datatypes#Bed http://wiki.galaxyproject.org/Learn/Datatypes#Interval Other issues with the column assignments could be a factor, but those would have most likely resulted in some sort of error. If this does not seem to address your problem and you would like more feedback, and are using the public Main Galaxy server, please submit a bug report: http://wiki.galaxyproject.org/Support#Reporting_tool_errors Take care, Jen Galaxy team On 12/7/12 7:32 PM, shamsher jagat wrote:

I have been trying to use Region variation > Make window but every time it returns empty file without any error I have a bed file of custom genome and has used

chrXX 1 10 0.23

Any suggestion please.

Thanks

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