when attempting to build an index using bowtie-build on a fasta genome file that is 2.1 MB, it does not create the .rev files, it produces 1.ebwt 2.ewbt 3.ebwt 4.ebwt but not the rev files. This is my first time using bowtie, all the parameters are the default options. Thanks
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Hi plasticdeath,
Sorry, the reply is 3 years late.
I think you might be running bowtie-build with some *.fastq files, which would only generate 4 ebwt files;
Try *.fasta then you will get all 6 index.ebwt files you want.
Typically, we should run de-novo assembly softwares first to get the assemblied fasta file. Like Velvet, SOAPdenovo etc.
After de novo assembly, we could run Bowtie to generate index files, then run bowtie to do the alignment.
hope this reply would be ok.
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