Re: [MUMmer-help] problem in running mummer

[Adam P. <aph...@gm...>]

Hello,
The show-tiling program should only produce no output if there is
insufficient similarity between the contigs and the finished sequence. I
believe by default it requires that over 95% of the contig aligns to the
reference. This threshold can be adjusted with the -v option.

However, I prefer to use the 'delta-filter' program to map contigs to a
reference sequence.

> nucmer -maxmatch ref.fasta qry.fasta
> delta-filter -q out.delta > out.filter.delta
> show-coords -qcl out.filter.delta > out.coords

This will generate the coordinates of the best matches for each contig to
the reference.

Best,
-Adam


On Fri, Oct 2, 2009 at 2:26 AM, HANG LI <li....@gm...> wrote:

> hello,
> I got to know mummer when received a work to map contigs to a finished
> sequence in my lab.The installation is pleasant,however,something went
> wrong when running it.
>     I successfully got the delta file and coords file ,but the
> tiling file was always empty ,and the mapview  can't use the coords
> file to create a image.I wonder if something wrong about my
> installation or my input file,will you please help me?the following is
> what displayed on my terminal.the delta file , coords file and cluster
> file was put in the accessory case.
>    Best wishes to you !
>
>
> lihang@lihang-desktop:~$ nucmer --prefix=1 5a.fasta c58circle.fasta
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "1.ntref" of length 5786248
> # construct suffix tree for sequence of length 5786248
> # (maximum input length is 536870908)
> # process 57862 characters per dot
>
> #....................................................................................................
> # CONSTRUCTIONTIME /usr/bin/mummer 1.ntref 25.25
> # reading input file "/home/lihang/c58circle.fasta" of length 2841580
> # matching query-file "/home/lihang/c58circle.fasta"
> # against subject-file "1.ntref"
> # COMPLETETIME /usr/bin/mummer 1.ntref 35.86
> # SPACE /usr/bin/mummer 1.ntref 8.41
> 4: FINISHING DATA
> lihang@lihang-desktop:~$ show-coords -rcl 1.delta > 1.coords
> lihang@lihang-desktop:~$ mapview -n 1 -f pdf 1.coords
> 00002   507305
> 00003   19204
> 00006   553132
> 00007   1445
> 00009   3528
> 00022   633784
> 00023   1181
> 00024   768341
> 00025   276095
> 00026   132848
> 00028   749260
> 00029   21075
> 00036   390647
> 00180   380781
> 00182   608
> 00183   101
> 00185   197
> 00186   593
> 00188   362075
> 00189   254458
> Incorrect object code at line 738
> lihang@lihang-desktop:~$ show-tiling 1.delta > 1.tiling
>
>
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