visualization of identified SSRs

Question

[kk.mahsa]

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?

[Titus]

You should precise your output file format

Answer 1

[Malcolm.Cook]

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.

Answer 2

[Farbod]

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!