cannot find SortMeRNA rRNA databases
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5.2 years ago
franzi ▴ 10

I have installed SortMeRNA using conda (manual see here:http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v2.0.pdf). SortMeRNA can remove reads that map to rRNA sequences. The tool says that it comes prepackaged with a set of rRNA databases. They are supposed to be located in a folder called "sortmerna/rRNA_databases".

I have found two paths which could potentially lead to this folder,

./anaconda2/pkgs/sortmerna-2.0-0
./anaconda2/bin/sortmerna

However, non of these paths contains a subfolder named "rRNA_databases". Also using find . -type d -name "rRNA*" at the highest level of my file system does not give any results.

Why can't I find the databases? Is it possible that the conda install version cames without these database files? Sorry for the potentially stupid problem.

RNA-Seq SortMeRNA rRNA databases • 3.0k views
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5.2 years ago
5heikki 9.9k

I imagine you can get the dbs from here

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Thanks very much! That's one way to fix this, however, I am still wondering why the installation does not seem to contain the databases. I don't find any of the subfolders listed in fig. 1 of the manual http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v2.0.pdf

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Manual may be the last thing developers update when they are releasing new code, especially when it is a small team. Perhaps an older version did come with packaged database but it does not anymore. Or the developer may have overlooked including it in the installer.

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