Assaf,
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
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
