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Old 08-21-2014, 04:19 PM   #1
Junior Member
Location: Brazil

Join Date: Aug 2013
Posts: 9
Default Bowtie-build index file generation, no *.3.ebwt, *.4.ebwt [2]

I am with the a similar problem that this guy:


Any ebwt file are being generated. But I am not using the -r option.

The command I am using is

bowtie2-build -f Mus_musculus_primary.fa Musmusculus

Only bt2 files are being generated. Can someone help me? I appreciate a lot.
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Old 08-21-2014, 11:43 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You're using bowtie2, so there won't be any *ebwt files produced (those are specific to bowtie1). You should just get 6 bt2 files.
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