Archer Analysis utilizes BWA and Bowtie 2 for mapping to hg19. Any read that has an Alignment Score less than 30 is removed from consideration. Reads with a mapping quality less than 30 are either multiple mapping reads or contain many low-quality bases (low FASTQ base quality). For the exact calculation of the mapping quality and the factors involved, please refer to the BWA and Bowtie 2 documentation. Note that this default value can be adjusted by the user under Analysis Settings in Archer Analysis.
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