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Old 10-01-2014, 11:24 AM   #3
JeffDu
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Location: durham

Join Date: Oct 2014
Posts: 1
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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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