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Old 05-27-2010, 11:48 AM   #1
David Lyon
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Default Filtering multi hits from sam file

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
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Old 05-27-2010, 12:18 PM   #2
thinkRNA
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Default

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.
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