Question: visualization of identified SSRs
0
gravatar for kk.mahsa
10 months ago by
kk.mahsa70
kk.mahsa70 wrote:

hi

i used MISA (MIcroSAtellite identification tool) to SSRs of whole genome. Now i want to visualize my output, How can i do it? any program or package do it?

visualize ssr • 351 views
ADD COMMENTlink modified 10 months ago by Farbod3.1k • written 10 months ago by kk.mahsa70

You should precise your output file format

ADD REPLYlink written 10 months ago by Titus720
1
gravatar for Malcolm.Cook
10 months ago by
Malcolm.Cook800
kansas, usa
Malcolm.Cook800 wrote:

Assuming the output format is as presented here, it looks like the output is in GFF format.

The next question is, what do you mean by "visualize"? If you want to see where all these SSRs fall on the genome with respect to other annotations (genes, repeative regions, etc), you will want to load the GFF file into a genome browser. Depending on what organism you are working with, there may be one already available for you at UCSC or Ensembl or NCBI.

ADD COMMENTlink written 10 months ago by Malcolm.Cook800
1
gravatar for Farbod
10 months ago by
Farbod3.1k
Toronto
Farbod3.1k wrote:

Dear @kk.mahsa, Hi,

To my best knowledge there are not any specific software to just prepare an eye-catching graph of MISA results, may be because the nature of outputs are not capable to "visualize" in a fancy manner,

I have seen that authors use excel to draw a pie-chart and/or a table of result. Bar-chart would be another choice.

~ Best

NOTE: these are the ways that SSRs discovered in RNA-seq is represented, maybe for whole-genome there is another story!

ADD COMMENTlink written 10 months ago by Farbod3.1k
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