Being from IIT Patna, you can expect a bit biased answer.
I do not have much idea about IIT Jodhpur but I can certainly vouch for the fact that IIT Patna has better infrastructural facilities than IIT Jodhpur since we have been in our Permanent campus for past two years and IIT Jodhpur has recently shifted to their new campus just recently so it would take time for them to adjust to the new setting.
Closing rank for 2016 for IIT Patna : 2774
Closing rank for 2016 for IIT Jodhpur : 2704
IIT Patna has approximately 10 more seats in CSE Deptt. than IIT Jodhpur ( I am not aware of the 2017 Seat Matrix though )
In the 2017 NIRF Ranking, IIT Patna has performed far better than IIT Jodhpur
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