Re: [MUMmer-help] Dear mummer group:About mummerplot questions (Clarence Hsiang)

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

Hello,
Those are all small repetitive alignments, which are occluding the other
alignments. Try running:

> delta-filter -m 191212mummer-10xNanko_oldPmref.delta >
191212mummer-10xNanko_oldPmref.mdelta
> mummerplot 191212mummer-10xNanko_oldPmref.mdelta --postscript

Which should clean up the plot quite a bit.

Best,
-Adam


On Thu, Dec 12, 2019 at 9:33 AM <r00...@nt...> wrote:

> Dear mummer group:
>
> Good evening.
>
> Japanese apricot (Prunus mume) is our research specie, and we
> conducted 10x genomics technique making a new genome by using genomic
> DNA from Japanese cultivar.
> Furthermore, we would like to compare the genomic difference between
> publised Prunus mume genome (chinese cultivar) with the new
> 10xgenomics Prunus mume genome.
>
> But the result of mummerplot showed very strange from the demo picture
> from the mummer tutorial website.
>
> The steps we used as below:
> nucmer -p 191212mummer-10xNanko_oldPmref
> /data/share/genome/pmum/old-with/annotation-until2018/P.mume.genome.fa
>
> /data/public/hsiang/10x_sequencing/190812-test1-result/output_0817_prefix.1.fasta
> mummerplot 191212mummer-10xNanko_oldPmref.delta --postscript
> And the output files as below:
> out.ps
> out.rplot
> out.gp
> out.fplot
> 191212mummer-10xNanko_oldPmref.delta
>
> FILES LINK:
> https://drive.google.com/open?id=1wH1Xpt8r4MiZ050UPWWu0mUkeJFpZEqH
>
>
> Could you give me some solutions and suggestions?
>
> Thank you very much
>
> Best wishes,
>
>
> Clarence Hsiang
>
>
>
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