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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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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. -
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.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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