Sorry about the oversight. Thanks for pointing it out. The file is now up on the FlyBase ftp site:ftp://flybase.net/flybase/associated_fi ... counts.txt
The publication report for FBrf0212682 will also be updated to have a link to this file (as of FlyBase release 2012_02).
P.S. The first four columns in the file are Junction_ID (format: chr_start_stop), chromosome, start, stop, followed by a read count and entropy score column for each sample. The samples are labeled in the table using BS numbers which have the following translations (note that the columns are not necessarily presented in this order):