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hzi-bifo / RiboDetector

Accurate and rapid RiboRNA sequences Detector based on deep learning
GNU General Public License v3.0
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no rRNA sequences were detected in an almost complete genome #11

Closed ThomasYJK555 closed 2 years ago

ThomasYJK555 commented 2 years ago

Hi, I am with great doubt with the accuracy of "RiboDetector" as a new user since I made a test for my metagenomic-assembly -genomes (MAGs). Several MAG from my previous binning and dRep work with the completeness of >95 and contaminant of <5 were selected for the rRNA detection test in "RiboDetector", the scripts are as follow (taking "MAG2809_RMAG1998.fa" as an example): ribodetector_cpu -t 20 -l 150 -i /data2/yjk/Bison_meta/rRNA/bin_for_test/MAG2809_RMAG1998.fa -r /data2/yjk/Bison_meta/rRNA/bin_for_test/rRNA/MAG2809_RMAG1998_rRNA.fa -e both -o /data2/yjk/Bison_meta/rRNA/bin_for_test/nonrRNA/MAG2809_RMAG1998_nonrRNA.fa 1>/data2/yjk/Bison_meta/rRNA/bin_for_test/MAG2809_RMAG1998.o 2>/data2/yjk/Bison_meta/rRNA/bin_for_test/MAG2809_RMAG1998.e

the error file indicated no rRNA sequence were detected

image

and the output file is empty too. Could any give me an interpretation? Many thanks in advance! Best regards, Jiangkun Yu

dawnmy commented 2 years ago

Hi Jiangkun Yu,

Thank you for your interest in RiboDetector. Our method is not designed for rRNA gene annotation for genomes. It is usually for identifying rRNA reads from sequencing data. To annotate rRNA gene in genome, you can try barrnap https://github.com/tseemann/barrnap. I hope this helps.

Best wishes, Zhi-Luo

ThomasYJK555 commented 1 year ago

Hi Zhi-Luo: Thanks a lot for your interpretation, now I've got it and greatly appreciate your recommendation for the method of rRNA gene annotation in genomes. Many thanks, Jiangkun

On Fri, Mar 25, 2022 at 5:14 PM Z.-L. Deng @.***> wrote:

Hi Jiangkun Yu,

Thank you for your interest in RiboDetector. Our method is not designed for rRNA gene annotation for genomes. It is usually for identifying rRNA reads from sequencing data. To annotate rRNA gene in genome, you can try barrnap https://github.com/tseemann/barrnap. I hope this helps.

Best wishes, Zhi-Luo

— Reply to this email directly, view it on GitHub https://github.com/hzi-bifo/RiboDetector/issues/11#issuecomment-1078810829, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVL7METFZGDGA7RP2SGJJF3VBV7YJANCNFSM5RS4D7AQ . You are receiving this because you authored the thread.Message ID: @.***>