Question: How to map a set of genes on a circular representation of DNA ?
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gravatar for CriticalPeriod
6 months ago by
CriticalPeriod0 wrote:

Hello everyone, I was wondering if it is possible to map all the genes that I found to be differentially expressed on a circular representation of the genome ? I've seen this kind of representation for atac or chip seq but I don't manage to find how to make one ?

It would be to visualize if the genes I found differentially expressed are located prefentially on some regions close in contact. Thank you very much, David

rna-seq • 213 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by CriticalPeriod0

Thanks ! It looks like possible with this, even though quite complicated but I'll look into it. Just to precise, I do not work with circular so in fact any other way of mapping (such as little chromosome schemes that I've seen recently) is appreciated. Thank you !

ADD REPLYlink written 6 months ago by CriticalPeriod0

Karyoplot R worked just fine, even though less clear than Circos that I didn't manage to install :'( Thank you both

ADD REPLYlink written 6 months ago by CriticalPeriod0
1
gravatar for darbinator
6 months ago by
darbinator220
darbinator220 wrote:

Maybe Circos ? http://circos.ca

I have never used it but it seems that we can do a lot of things

ADD COMMENTlink written 6 months ago by darbinator220
1
gravatar for palabari
6 months ago by
palabari10
palabari10 wrote:

you could also try: https://bioconductor.org/packages/release/bioc/vignettes/karyoploteR/inst/doc/karyoploteR.html

ADD COMMENTlink written 6 months ago by palabari10
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