Question: How can I map certain values for gene locus against genome?
0
gravatar for MAPK
10 months ago by
MAPK1.4k
United States
MAPK1.4k wrote:

I have a data like below. I want to make a plot where I want to map each locus to the genome sequence (Chr 1..15 as X axis) and show the counts in Y axis. How can I create that type of plot? Is there any bioconductor package to do this?

locus   counts
SS1G_03009  40

SS1G_02499  10

SS1G_09248  10

SS1G_09768  22

SS1G_04468  22

SS1G_08838  11

SS1G_02828  23
R • 327 views
ADD COMMENTlink written 10 months ago by MAPK1.4k
2
gravatar for genomax
10 months ago by
genomax71k
United States
genomax71k wrote:

Manhattan plot using R?

ADD COMMENTlink written 10 months ago by genomax71k

Yes, that would do, but I need to get the chr, start and end information for the given loci. How can I extract that from NCBI or using genes and genome fasta files? Or using the package you have suggested, I would need BP variable, so I am not sure how I can obtain that.

ADD REPLYlink modified 10 months ago • written 10 months ago by MAPK1.4k
1

Recall the NCBI unix utils answers provided by @vvkodali to one of your past questions. You should be able to use that to get the info you are asking for above.

ADD REPLYlink written 10 months ago by genomax71k

Thank you so much, I just got it :)

ADD REPLYlink modified 10 months ago • written 10 months ago by MAPK1.4k
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