Biostar Beta. Not for public use.
Understanding MUMmer show-diff
1
Entering edit mode
5.3 years ago
Huggie • 20
Australia

I have many questions regarding the output of MUMMer's show-diff script. I've read description on show-diff -h as well as in the README of the top-level directory. However I do not understand the output. I'll start with GAP reported by show-diff.

According to README:

[GAP] A gap between two mutually consistent ordered and
oriented alignments. gap-length-R is the length of the
alignment gap in the reference, gap-length-Q is the length of
the alignment gap in the query, and gap-diff is the difference
between the two gap lengths. If gap-diff is positive, sequence
has been inserted in the reference. If gap-diff is negative,
sequence has been deleted from the reference. If both
gap-length-R and gap-length-Q are negative, the indel is
tandem duplication copy difference.

I made the following illustration trying to understand it.

I do not understand what it means by "If both gap-length-R and gap-length-Q are negative, the indel is tandem duplication copy difference, and how that is different from the reported DUP. Any help is appreciated, thanks.

MUMMer • 2.0k views
ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1