[GenoMax]

Dear Genomax,
When i mentioned the --prefix to give the path the it was showing the following:
./tophat --prefix= /home/me/Downloads/bowtie2-2.2.3/bowtei/ /home/me/Downloads/bin/Sample_L1_R1_trim.fastq
tophat: option --prefix not recognized
for detailed help see http://tophat.cbcb.umd.edu/manual.html


then what should i do?

What is the "prefix" of your bowtie2 index files? Where are those files located?

BTW: When you run TopHat you do not need to add "--prefix" to the name of the index files. Your original command line was ok. Just did not have the right prefix name.