It is in fastq format and following QC filtering with fastx I end up single reads that no longer have a pair. It seems that these single reads are messing up my assemblies in velvet. Recently, I tried using sickle to filter and it seems to have resolved the issue.
Thanks for the help.
Picard tools has a handy webpage for working out the meaning of SAM flags (and combinations of flags):
These can be used with 'samtools view -f N', where N is the flag you want to filter your reads with.
E.g. to extract all the properly paired reads:
samtool view -S -f 2 -o proper-paired-reads.sam input.sam