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Old 08-10-2015, 08:06 AM   #4
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978

When things are not in the current directory (or in $PATH) it is simple to provide the full/relative path to the file/directory in question.
$ bowtie2-build ./hg19.fa hg19 OR
$ bowtie2-build /home/dnascopev/Desktop/hg19_fasta/hg19.fa hg19
Is there a reason your are building these yourself than getting them from iGenomes?
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