Filtering multi hits from sam file

David Lyon · 05-27-2010, 11:48 AM

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 · 05-27-2010, 12:18 PM

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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05-27-2010, 11:48 AM	#1
David Lyon Member Location: USA Join Date: May 2010 Posts: 11	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

05-27-2010, 12:18 PM	#2
thinkRNA Member Location: Carlsbad,CA Join Date: Jan 2010 Posts: 94	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.