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Old 06-10-2011, 08:27 AM   #1
madsaan
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Location: california

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Exclamation tophat hg19 index

Hi,

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?

Thanks,
Joji
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Old 06-10-2011, 09:56 PM   #2
Jon_Keats
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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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