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Old 06-19-2012, 09:17 AM   #4
GenoMax
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Join Date: Feb 2008
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You build the index for the reference genome (and not for a particular type/length of reads).

I think you may be confused by the wording in the first para here (http://bowtie-bio.sourceforge.net/ma...what-is-bowtie). The 36-bp is a historical reference to the original read length for illumina reads (which have since been lengthened to 150 bp or more).

Last edited by GenoMax; 06-19-2012 at 09:19 AM.
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