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Old 11-21-2012, 03:03 AM   #1
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Join Date: Jun 2012
Posts: 59
Default RIbopicker optimum parameters?

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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ribopicker, rna-seq

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