Merging RNA-seq replicates from Tophat

Sometimes, you might want to present your replicates as one consensus sequencing track on viewers like IGV or IGB.

To merge bam files : Use samtools merge.
To merge junctions.bed files : Use the tbedjuncs and combineJuncs scripts at seqscripts

cat junctions_file1.bed junction_file_2.bed junction_file_3.bed | tbed2juncs | combineJuncs > combined.junctions.bed

Ref: http://seqanswers.com/forums/showthread.php?t=3381