SRA format needs to be converted into fastq to be used as input to Bowtie, Tophat etc. Here is how:
1. Download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
If you are using 64-bit linux, try the CentOS Linux 64 bit architecture first. It is so much pain to compile from source.
Decompress the downloaded file, and copy the fastq-dump file to system path.
Convert SRA to fastq
bash fastq-dump <SRA archive file>which will create a fastq file with the same name as the SRA archive file.