Bowtie-build index file generation, no *.3.ebwt, *.4.ebwt [2]

[seqador]

I am with the a similar problem that this guy:

"http://seqanswers.com/forums/showthread.php?t=3422"

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.

[dpryan]

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.