RSEM v1.1.5 is online now (http://deweylab.biostat.wisc.edu/rsem/).
Several bugs are fixed. One critical bug relates to set the correct
probability of generating a read from forward strand. If users let RSEM
run bowtie and do not set the "--strand-specific" option, the bug would
make RSEM throw all alignments aligned to forward strand away (by setting
the "--forward-prob" as 0). The other two are related to confidence
interval calculation. These bugs exist since RSEM v1.1.0. It is important
for users to update to this version.
Best,
Bo