tophat

  104   nohup tophat -r 124 -o tophat124  --num-threads=4 hg19 AGS_1_sequence.fastq  AGS_2_sequence.fastq >screen.txt &

The estimated library average fragment size is 280, the read length is 60bp, so the inner distange between paired reads (--mate-inner-dist) is 160.

124=fragment size(insert size) - 2*read length