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Difference between mate pair and pair end

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  • Difference between mate pair and pair end

    Hi All,

    i am confused between two terminology Mate paired and Pair end. Please help me out on this.

    Thanks

  • #2
    Even i have a doubt regarding 'mate-pair inner distance' parameter option -r which is essential to give while running tophat with pair-ends.

    Can someone help me how to determine the mate-inner-dist (-r) if i know the reads size but not the fragment size.
    For example if my reads length (paired-reads) is of length 50 bp and in another set the reads length (paired-reads) is 45 bp.

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    • #3
      Originally posted by bassu View Post
      Hi All,

      i am confused between two terminology Mate paired and Pair end. Please help me out on this.

      Thanks
      A search of the forum reveals this thread http://seqanswers.com/forums/showthr...ight=Mate+pair

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