A large list of chromossome

Question

[1996luanabianca]

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)

[Bastien Hervé]

Please give us a look of the inside of felis_catus_chrom variable

[1996luanabianca]

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).

[Bastien Hervé]

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.

[1996luanabianca]

i will look. Thanks very much!!!!

Answer 1

[JC]

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