rRNA output systematically emtpy

[plger]

Hi, Thanks for the great tool. I'm using your Mus Musculus annotation (and -r $ref/rRNA_db/mouse_rRNA) with standard truseq small rna data, and there's never any overlap detected with rRNA_db annotation: the _processed/*_output_rRNA_* are empty (but there), and in the _result/*_summary.txt file there are (many) reads assigned to ensembl-rRNA and Rfam-rRNA, but nothing from rRNA_db. The processing_report/*.txt is empty in that section, and has no other indication except plotting errors at the end, i.e.:

match to rRNA database

match to tRNA database

[...]

generating graph
Error: No enough input parameters!
Execution halted
Error: No enough input parameters!
Execution halted

It seems difficult to imagine that there would really be no trace of the 4S/5S/etc (across many samples)... Looking at the different annotation subfolders, I noticed that while all annotations have a single bowtie index (i.e. prefix), rRNA_db has several - could the problem stem from this?

Any pointer on how to debug this would be appreciated.

[junchaoshi]

Hi plger,

Yes, most datasets should contain rRNAs. And the rRNA annotation fold indeed contains several rRNA bowtie indexes for rRNA annotation strategy. The error showed in the report means you used the -r parameter but no data generated. However, according to your description, I can only suggest you redownload the database.

[plger]

Hi, don't know why I missed it yesterday: in your documentation it says to use -r /<your_defined_address>/Mus_musculus/rRNA_db/mouse_rRNA, but actually in the annotation you created the folder is rRNAdb, not rRNA_db (you might want to change the readme!). Then it works like a charm. Thanks,

[junchaoshi]

Hi plger,

Good to know you have debuged.