Closed plger closed 5 years ago
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.
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,
Hi plger,
Good to know you have debuged.
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 withrRNA_db
annotation: the_processed/*_output_rRNA_*
are empty (but there), and in the_result/*_summary.txt
file there are (many) reads assigned toensembl-rRNA
andRfam-rRNA
, but nothing from rRNA_db. Theprocessing_report/*.txt
is empty in that section, and has no other indication except plotting errors at the end, i.e.: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.