Question: A large list of chromossome
0
gravatar for 1996luanabianca
9 months ago by
1996luanabianca0 wrote:

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)

dataframe chromossome list R • 217 views
ADD COMMENTlink modified 9 months ago by zx87548.4k • written 9 months ago by 1996luanabianca0

Please give us a look of the inside of felis_catus_chrom variable

ADD REPLYlink written 9 months ago by Bastien Hervé4.5k

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).

ADD REPLYlink written 9 months ago by 1996luanabianca0

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.

ADD REPLYlink written 9 months ago by Bastien Hervé4.5k

i will look. Thanks very much!!!!

ADD REPLYlink written 9 months ago by 1996luanabianca0
0
gravatar for JC
9 months ago by
JC9.1k
Mexico
JC9.1k wrote:

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

ADD COMMENTlink written 9 months ago by JC9.1k
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