difference between microsatellite markers

Question

[elvanbaskurt4848]

Hi, Is there any difference between Illimuna-genomic sequence based microsatellite (SSR) markers and transcriptomic sequence based ones? If so, could you please explain the difference.

Thanks in advance, Elvan

[Buffo]

SSR from transcriptomic data? How it is possible if they are from non-coding regions? I think you can (or have) do this analysis just for reads from genomic sequences.

[elvanbaskurt4848]

Actually transcriptome based SSR markers are named as EST-SSR or genic-SSR, such as "https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-11-17". However I have same question, I couldnt understand the logic behind genic-SSRs. How possible to use them directly for amplification from DNA?. Additionally what is the difference between genomic and genic SSRs to distinguish them? Thank you, Elvan

[WouterDeCoster]

Please useADD REPLY to reply to earlier reactions, as such this thread remains logically structured and easy to follow. I have now moved your post, but as you can see it's not optimal.

[Buffo]

Genomic includes non-coding regions, genic does not (even 5and 3 UTRs).

[elvanbaskurt4848]

thus we can say that genic SSRs are more specific than genomic ones. However I think genomic SSRs must be more comprehensive, what I understand. Thank you.