Question: Regional Variation Make Windows Output
gravatar for odhardy
21 months ago by
odhardy10 wrote:

i believe there is an issue with make windows tool: i am attempting to create sliding windows on a set of intervals, however some valid windows seem to get tossed from final output as offset increases.

example input interval: chr1 0 681

example window, 120bp, offset 120bp: in this case I get the expected result chr1 0 120 chr1 120 240 chr1 240 360 chr1 360 480 chr1 480 600

example 120bp window, 240bp offset, result:

chr1 0 120 chr1 240 360

this is not what I would expect because the below interval is still valid, as output in first example. The offset and window size are still within the input boundary

chr1 480 600

example 120bp window, 360bp offset:

chr1 0 120

again now TWO valid intervals are rejected. I have not found precise pattern yet, however I see the issue in multiple datasets and occurs as the offset size approaches twice the window size. When windows are "end to end" or overlap the output is as expected.

intervals windows • 410 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by odhardy10
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The offset size should be smaller than the window size when using this tool. This is an older tool and does not cover alternate use cases.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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