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explanation about hard clip and soft clip reads

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  • explanation about hard clip and soft clip reads

    Hello Everyone,

    I am working on SOLiD data. I am using Lifescope v2.5.1 for mapping of reads. SAM file obtained after mapping contains CIGAR string in form of hard clip and soft clip.

    I was just wondering that if in a 75bp read CIGAR string is 34H41M or 49M26H then will this be considered as bad mapping or still we can consider this as good mapped read. Is there a limit on number of hard clip or soft clip present in the sequence.

    Hoping for a positive response.

    Thanks in advance

    Neha

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