Question: How can I map certain values for gene locus against genome?
0
gravatar for MAPK
4 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 • 219 views
ADD COMMENTlink written 4 months ago by MAPK1.4k
2
gravatar for genomax
4 months ago by
genomax63k
United States
genomax63k wrote:

Manhattan plot using R?

ADD COMMENTlink written 4 months ago by genomax63k

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 4 months ago • written 4 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 4 months ago by genomax63k

Thank you so much, I just got it :)

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