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A large list of chromossome

Hi.

I split Felis catus genome by chromossomo. 

felis_catus_chrom <-split(felis_catus_Anotations, felis_catus_Anotations$CHROM)

Now, I have a large list with 132 elements (each one a chromossome) and I would like make a dotplot grafic from InDels. How can I do that? (sorry, I'm dummie in bioinformatics)

chromossome dataframe list r
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updated by zx8754 zx8754 • written by 1996luanabianca • 1996luanabianca

Please give us a look of the inside of felis_catus_chrom variable

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written by Bastien Hervé Bastien Hervé

Sorry, I forgotten to say.

My data frame is a .vcf file and i would like to do a plot the columm 2 (Position) and columm 9 (InDels).

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written by 1996luanabianca • 1996luanabianca

I can suggest you to take a look at karyoploteR. I use it a lot to display information on chromosomes. There is a Plot SNP array raw data tutorial that produces a result really close to what you want.

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written by Bastien Hervé Bastien Hervé

1 answer

For your code I believe you're using R for this, you can use the dotPlot function of the seqinr package https://www.rdocumentation.org/packages/seqinr/versions/3.4-5/topics/dotPlot

Alternatively, you can use the dot plot programs in EMBOSS http://emboss.sourceforge.net/apps/cvs/emboss/apps/alignment_dot_plots_group.html

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written by JC JC

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