12 Apr
2011
12 Apr
'11
12:58 a.m.
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. ).