Extract paired-end reads from single SRA file

for paried-end (Layout: PAIRED) data in 1 sra file, use the following command:

fastq-dump the_sra_file --split-3 -O the_output_directory

This will give you 2 (or 3) fastq files:
file_1.fastq - mate parie forward strand
file_2.fastq - mate pair reverse strand
file.fastq - reads without mate pair.

Remeber to use most up-to-date SRA took kit, it will reduce a lot of problems:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software