tophat hg19 index

[madsaan]

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

[Jon_Keats]

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)