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
-
-
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
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM
Comment