How can I map certain values for gene locus against genome?
1
0
Entering edit mode
6.0 years ago
MAPK ★ 2.1k

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 • 1.2k views
ADD COMMENT
2
Entering edit mode
6.0 years ago
GenoMax 147k

Manhattan plot using R?

ADD COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

Thank you so much, I just got it :)

ADD REPLY

Login before adding your answer.

Traffic: 2288 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6