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madsaan 06-10-2011 08:27 AM

tophat hg19 index

I was wondering if it is ok to use the pre built hg19 index from Tophat for BWA as the reference genome or should I build an index by myself?


Jon_Keats 06-10-2011 09:56 PM

For BWA you will need to build a new one the TopHat (aka bowtie) index will not work. Human hg19 build takes around 3 hours on a typical system. For genome source I'd suggest the 1000 genomes version of GRCh37 (aka hg19)

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