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SmallRNA Seq Analysis

Hi, I have some smallRNA-seq samples and I used srnabench tool online. But I have a Problem. For all samples, Of the total number of reads only 1% of reads are taken as input and used in the analysis. Is this normal? What are the filters that srnabench does? and the mapping parameters? How can I make the tool take all the input reads? Help me, thanks. Giovanna

sequencing

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