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plasticdeath 10-11-2011 11:32 AM

bowtie build does not create .rev index files
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

plasticdeath 10-11-2011 12:04 PM

if there is any other information you need to help me with this issue, please let me know. I have a 64 bity system with 2GB of ram and 65 GB of hard drive space free. I am using the latest 64 bit version of Ubuntu linux.

JeffDu 10-01-2014 11:24 AM

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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