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Old 09-24-2009, 07:05 AM   #1
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Location: USA

Join Date: May 2009
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Default Using Maq with TopHat

Is it possible to use Maq with the latest version of TopHat? I would like to use Maq to align my reads to a reference genome. Then I would like to use TopHat to call RPKM based on the Maq alignments and a supplied GFF3 file. I think the original version of TopHat used Maq as the alignment program, but the current version used Bowtie. Does anyone know what needs to be done to use the Maq output as the alignment in TopHat?
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