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  • Mapping Hiseq X ten reads

    Hi there!
    I'm working with data of the new Illumina Hiseq X ten for resequencing (human) individuals (paired-end). The reads quality is now given in bins instead of regular Q-scores.
    Has anyone experience in mapping that kind of reads?
    Is there any influence of the new quality bins in the mapping procedure, since several programs use the quality score for accurate mapping?
    I know the Isaac-mapper does deal with this, since it is an Illumina specific tool. When I compared the results of Isaac with BWA (with default settings) I get big differences in percentage of mapped reads (much less in BWA).

    May be some one has experience with this data?
    It's my first time with Illumina data, so I would appreciated any advice!
    Thank you very much!
    Cheers

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