Question: cannot find SortMeRNA rRNA databases
1
gravatar for franzi
2.8 years ago by
franzi10
franzi10 wrote:

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.

ADD COMMENTlink modified 2.8 years ago by 5heikki8.4k • written 2.8 years ago by franzi10
0
gravatar for 5heikki
2.8 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

I imagine you can get the dbs from here

ADD COMMENTlink written 2.8 years ago by 5heikki8.4k

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

ADD REPLYlink written 2.8 years ago by franzi10

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.

ADD REPLYlink written 2.8 years ago by genomax65k
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