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  UGENE Forum › General Category › Help and How-to › Prebuilt Index in Bowtie2
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Prebuilt Index in Bowtie2 (Read 28360 times)
Oct 3rd, 2014 at 9:08pm

CGR   Offline
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I am trying to align short reads with Bowtie2 and a prebuilt index.  I have checked the box "Prebuilt Index", but it still requires a reference sequence to proceed.  I can't select the folder that contains the 6 files that make up the reference, and I have tried choosing individual .ebwt files, but that doesn't work either. 

How do I align to a prebuilt index?
 
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Reply #1 - Oct 6th, 2014 at 6:31pm

Olga Golosova   Offline
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Hello,
Bowtie2 index files have .bt2 extension, .ebwt files are index files for the first Bowtie. Maybe, this is why the problem occurs. If not, could you please specify the UGENE version that you use (Windows/Mac OS/Linux; 32-bit or 64-bit; standard/full/NGS package) - currently, I can't reproduce the problem on my computer.
 
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