Hi all, I'm using Ribopicker to remove rRNA sequences from RNA-Seq data but so far the amount of sequences being identified as rRNA seems to be very low (considering that >90% of the RNA is supposed to be rRNA) even in samples which haven't received any sort of treatment to reduce the rRNA content before cDNA library creation and sequencing. The parameters which I've used so far are -c (Alignment coverage threshold in percent. ) 50 -i (Alignment identity threshold in percent. )70 and -l (Alignment length threshold in percentage) 30. FYI The samples I'm looking at contain both human and bacterial rRNA. Any help would be appreciated.
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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