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How to filter reads on PHRED score

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  • How to filter reads on PHRED score

    Hi all,

    I am new to RNA-seq analysis. So sorry if you feel I am asking a basic question. How to filter raw sequencing reads (74 nucleotides in length) based on their PHRED quality scores to get reads having a certain base-call accuracy, which I can use for alignment to the genomic sequence and then get a list of uniquely mapped, partially mapped and unmapped list.

    Thank you