explanation about hard clip and soft clip reads

[neha]

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