Trimming for RNA-Seq data

Quality trimming decreases the overall number of reads, but increases to the total and proportion of uniquely mapped reads. Thus, you get more useful data for downstream analyses. Too aggressive quality trimming can negatively impact downstream analysis (in our example, estimation of gene expression). Hence, our own findings and that of the research community motivate the incorporation of a light amount of trimming in RNA-seq data (we use a Q threshold of 10).

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