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Old 10-07-2015, 09:25 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
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As you have discovered the hard way it is extremely important to make sure that you are using a consistent genome build/patch level for your analysis (I assume that is what is being reflected in the co-ordinate differences above).

If you want to avoid these types of issues you could download sequence/annotation/index bundles (you will need to roll your own indexes if you want to use STAR but at least the sequence/annotation would be consistent) from iGenomes.

In terms of salvaging the analysis, check to see if there are corresponding annotation files available at NCBI where you got the sequence files.
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