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  • Naive question about Cuffdiff log

    I have been looking at posts about following question and could not find a convincing answer.

    In the logs generated by cuffdiff , we saw following lines:
    -----------------------
    Map Properties:
    > Normalized Map Mass: 24669329.12
    > Raw Map Mass: 22464890.18
    > Number of Multi-Reads: 487240 (with 1308767 total hits)
    > Fragment Length Distribution: Empirical (learned)
    > Estimated Mean: 141.07
    > Estimated Std Dev: 44.85
    --------------------

    Here does fragment length refers to the size between two pairs, or length of total fragment, including both reads and insert between them.

    For this specific example, if I have 80 bp reads at each side, does that mean they overlap, or is there 140 bp in the middle?

    Thanks

  • #2
    it means they overlap. most tools talk about insert size or fragment length which means the full length of the aligned fragment. mine usually overlap as well.
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

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