SK_phase2_tfgs_final is the transfrags bed file
with the trascribed fragments description for
the April 2003 release of the human genome (hg15).
The score field inidicates the quality of the tranfrag:
   0 - Passes all filters
   1 - Overlaps a pseudogene
   2 - Overlaps a blat hit
   3 - Overlaps both a pseudogene and a blat hit.

The method used to generate these transfrags is as follows:
   A threshold of 13.93 (which gives an average FP rate of ~ 0.05 in negative bacterial controls)
   was applied to all the signal graphs and defined coordinates as positive.  Positive coordinates
   seperated by gaps less than or equal to 30bp were merged.  Resulting regions that were less than
   50bp in length were filtered out.  Finally, 12bp were added to all start coordinates and 13bp to 
   all stop coordinates (ie. interbase coordinates) which shifts the coordinates to be centered over 
   probes as opposed to being left justified with respect to probes as is the case in the 
   raw and graph data.