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From: Adam P. <aph...@gm...> - 2013-12-19 22:06:33
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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 > > > > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > > |