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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Prebuilt Index in Bowtie2 https://forum.ugene.net/forum/YaBB.pl?num=1412345305 Message started by CGR on Oct 3^rd, 2014 at 9:08pm

Title: Prebuilt Index in Bowtie2
Post by CGR on Oct 3^rd, 2014 at 9:08pm

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?

Title: Re: Prebuilt Index in Bowtie2
Post by Olga Golosova on Oct 6^th, 2014 at 6:31pm

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.