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About Insert, Insert size and MIRA mates.file

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  • About Insert, Insert size and MIRA mates.file

    Hello All,
    I am confused about what an Insert actually is ? And what is an insert size ?
    I am dealing with 454 paired end data. How is a Linker different from an Adaptor?

    I will be using MIRA's sff extract to extract the fasta and qual files from the sff files.
    So does the sff files have read info this way:


    i.e - Seq.forward - Linker - Seq.reverse ??

    In the above, what is an insert ? and whats the size ?
    So do each of the reads in an sff have the above format ?

    So in the MIRA's mates.file setup can I just use the following default format for the mate pairs ?

    pair (.*)\.f (.*)\.r

    Please help me out with my confusions:



  • #2
    In addition, in the Newbler metrics of the assembly, for a particular sff file it says about the 'pairedReadStatus'
    pairDistanceAvg = 2247.3
    pairDistanceDev = 561.8

    Now is this information about the assembly status or the raw reads status ?
    Is pairDistanceAvg the Insert size ????