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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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Classification of the rRNA removed seqeunces #45

Closed LeoVincenzi closed 6 months ago

LeoVincenzi commented 9 months ago

Dear developers, I have a question about the reads discarded by Ribodetector: can the software report which kind of rRNA sequences they contain (mammalian, bacteria, etc..)? Or which database would you suggest using to identify this information in the removed reads? Thanks for your help, Leonardo

dawnmy commented 9 months ago

You could map the output rRNA reads against SILVA database: SILVA_138.1_LSURef_NR99_tax_silva.fasta.gz and SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz using short reads aligner. Then you should be able to get the taxonomy information of the reads.

LeoVincenzi commented 9 months ago

Okay, thank you very much. By your experience, would you suggest using BWA or bowtie2?

dawnmy commented 9 months ago

I think they are similar, BWA has BWA-mem2 which might be good to try