Filtering multi hits from sam file

[David Lyon]

From the output of botwie-tophat how do I remove from the accepted_hits.sam file all hits that map mutiple places on the genome and leave those hits that map to one place only?

thanks

[thinkRNA]

One way to do this is to use the -g 1 option when running tophat which would suppress all reads that hit in more than 1 place.

Although, I am interested in knowing if there is a way to parse this information from the alignment. I don't know whether the SAM format has a flag for multi-reads.