Question: visualization of identified SSRs
gravatar for kk.mahsa
2.0 years ago by
kk.mahsa100 wrote:


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 • 674 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 2.0 years ago by kk.mahsa100

You should precise your output file format

ADD REPLYlink written 2.0 years ago by Titus910
gravatar for Malcolm.Cook
2.0 years ago by
kansas, usa
Malcolm.Cook1.1k 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 2.0 years ago by Malcolm.Cook1.1k
gravatar for Farbod
2.0 years ago by
Farbod3.3k 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 2.0 years ago by Farbod3.3k
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