Thanks for the quick answer,

Jeremy Goecks wrote, On 04/11/2011 12:50 PM:
>> Assuming cuffcompare generates a TMAP and REFMAP file for each
>> input file, does this mean the wrapper tool retrieves only the
>> first and second input files' TMAP and REFMAP files ?
> Yes, this is the way it works currently. This is clearly problematic,
> but it meets most users' needs as it enables them to generate a file
> of combined transcripts--which is needed for Cuffdiff--from many sets
> of Cufflinks' transcripts. 

I'm wondering if users are actually looking into those TMAP & REFMAP files, or 
can they be simply ignored ?
Ignoring them would make the tool much simpler (no symlinking patches, etc. ).

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