Re: [MUMmer-help] NUCmer - show-tilling

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

Hi Nelly,
show-tiling "pseudomolecule" option never quite does what people want it to
do. If I recall correctly, it tries to be too clever in determining the
offset of each contig in cases where the alignments don't extend to the
very end of the sequence. Also, when the layout of two contigs overlaps, it
will arbitrarily pick one or the other to fill sequence in the
pseudomolecule.

I'd recommend instead running:

*nucmer -maxmatch reference.fasta scaffold.fasta*

*delta-filter -q out.delta > out.filter.delta*

*show-coords -THrcl output.filter.delta > output.filter.coords*
That will find the "best" alignment of each query scaffold to your
reference and dump the alignments as a set of tab delimited intervals. From
that output, and the associated mummerplot, you should be able to
reconstruct the true tiling.

Since writing show-tiling many years ago I have shied away from building
automated "pseudomolecules" because they never get it quite right, and
there is no guarantee that the reference chromosomal structure is the same
in the new genome. If you really need a pseudomolecule, you should be able
to reconstruct the relative order and orientation of your scaffolds from
the coords output.

Best,
-Adam



On Tue, Dec 17, 2013 at 9:57 AM, DESPLAT, Nelly
<Nel...@bi...>wrote:

>  Hello,
>
> I have a draft genome with multiple scaffolds (≈800 Mb) and a reference
> genome (2.5Gb).
>
> I want to determine the position and orientation of these scaffolds in
> relation to my reference genome using nucmer (MUMmer3.22).
>
> Here are my command lines, according to the documentation page here (
> http://mummer.sourceforge.net/examples/#nucmer) :
>
> *nucmer -p output -mum reference.fasta scaffold.fasta*
>
> *delta-filter -i 90 -u 0 -q -r -l 100 output.delta > output.filter*
>
> *show-coords -rcl output.filter > output.filter.coords*
>
> *show-tiling -v 50 -g -1 -p output.fasta output.filter > output.tiling*
>
> For show-tilling, I used –p option to create a pseudo molecule with the
> scaffolds.
>
> I would like understand how this programm creates the pseudo molecules
> because I have observed strange things.
>
> For example, show-tilling give me this output file :
>
> *> Chr1 *
>
> *…*
>
> *4927886          4941005          35706  13120  87.17   99.70   +
> scaffold_27425*
>
> *4976712          4989443          -5294   12732  73.63   97.01
> +         scaffold_28410*
>
> *4984150          5029997          4990    45848  93.02   98.31
> +         scaffold_2130*
>
> *5034988          5036622          8513    1635    100.00 99.88
> +         scaffold_63004*
>
> *5045136          5052379          -1891   7244    97.87   96.75
> -           scaffold_44222*
>
> *…*
>
> But when I look at the sequence at these positions in the fasta file, I
> can see that some scaffolds are missing (scaffold_2130*) *or truncated
> (scaffold_27425*)*. The scaffold_2130 seems to be replaced by a gap of
> the size of the two gaps around this scaffold (4990 + 8513).
>
> Can you please tell me how the scaffolds are used to create the chromosome
> based on the information of the tilling file?
>
> Thanks for your help.
>
>
>
> Nelly Desplat
>
>
>
> Bioinformatics Engineer
> Upstream Genomics
>
> BIOGEMMA
> Route d'Ennezat
> Site de la Garenne
> CS 90126
> 63720 CHAPPES
>
> FRANCE
>
>
>
>
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