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Old 04-01-2011, 08:22 AM   #1
glacerda
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Location: Brazil

Join Date: Aug 2008
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Exclamation mapping tool for resequencing

Hi colleagues,
Is there any mapping tool that can deal with Illumina mate pair libraries (3Kbp insert, outwards) with up to 50% of paired end 400bp insert inwards contaminating reads?
I would like to use a tool that tries to map a read pair using both options for insert size and orientation. It is also desirable to include in the SAM the reads that map to the genome, even if its pair could not be mapped, flagging it with the proper bits. It is also desirable to include the information if the alignment is unique, multiple, etc.
Do you know any mapping tool that can do all that in just one run?

Thank you
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