miRDeep2 Mapper "Bowtie mapping tool not installed"
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Entering edit mode
19 months ago

I had created an index with bowtie (v1.1.0/gcc-4.8.5) and proceeded to using the mapper module of miRDeep which produced this error;

^[[1;31m
Error: ^[[0mBowtie mapping tool not installed.


I notice that the latest version of bowtie is 1.2.3, so is this a case of asking the administrator of our cluster to simply update the software to the latest version? Given that bowtie and not bowtie2 is specified in the original miRDeep2 paper, creating an index with bowtie2 will not fix the problem?

Thanks, Duncan

RNA-Seq miRNA bowtie • 398 views
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Entering edit mode
19 months ago
Barry Digby ▴ 790

Do not use bowtie2. From what I recall using the tool, you have to set quite a few paths in your ~/.bashrc file. One should point to the mirdeep2 bin, something like this:

export PATH=\$PATH:/home/barry/Desktop/Vivaldi/mirdeep2/mirdeep2-master/bin


In this folder are the bowtie executables.

An alternative (and cleaner option) is to use Anaconda to create an environment specifically for mirdeep2 which can be installed by calling:

conda create --name mirdeep2
conda activate mirdeep2
conda install -c bioconda mirdeep2


Hopefully the anaconda installation takes care of all the messy SQUID | randfold | vienna installations.

Try it via anaconda and run their test data!