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  • fongchun
    Member
    • May 2011
    • 55

    Expected Pair-end length parameter - GSNAP

    Hi,

    I apologize if this question has been asked, but I can't find any clarification on this question. I've gotten no replies on the gsnap mailing list about this unfortunately.

    I am looking at the --pairexpect parameter in gsnap:

    -pairexpect=INT Expected paired-end length, used for calling splices in medial part of paired-end reads (default 200)

    Is this referring to the inner-mate distance between the two paired-end reads? Or is it the expected insert size of the fragment that the paired-end reads are sequenced from (i.e. read length * 2 + inner-mate distance)? Or am I totally misinterpreting the meaning of this parameter?

    Any help would be appreciated.

    Thanks
  • jebowers
    Member
    • Apr 2013
    • 19

    #2
    I do not know this software but in general, for many software programs, paired end length is the whole size of the insert. Generally read*2+inter-mate distance.

    Comment

    • fongchun
      Member
      • May 2011
      • 55

      #3
      Originally posted by jebowers View Post
      I do not know this software but in general, for many software programs, paired end length is the whole size of the insert. Generally read*2+inter-mate distance.
      Thanks for the reply. You are right. I got a direct reply from the author and it is indeed the insert size.

      Comment

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