I have no problem estimating time for Stories, but if I create a sub-task for the story, I can't find anywhere that will allow me to estimate the sub-task time. Ideally, I will provide estimates for the sub-tasks and the sub-task estimates will bubble up to the Story level. Is there any way I can do this?
No. JIRA Agile does not have the concept of estimating on the sub-task level. You can Google around for different workarounds but this is Atlassian's comments (http://blogs.atlassian.com/2012/09/agile-qa-greenhopper-time-estimates-with-sub-tasks/).
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