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Old 08-10-2015, 10:47 AM   #12
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978

Wow .. my head is starting to hurt

Why did you put the bowtie2 executables under the directory with the fasta sequence? There is no logical explanation as to why this is not working .. perhaps bowtie does not like to have any other files/directories where it is working.

If you are willing .. try the following (I am assuming that the executable files are right in bowtie2-2.6.0 directory):

$ mv /home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0 /home/dnascopev/Desktop/
$ export PATH=$PATH:/home/dnascopev/Desktop/bowtie2-2.6.0
$ bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19
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