difference between microsatellite markers
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4.7 years ago

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

next-gen sequencing SSR • 1.3k views
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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.

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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

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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.

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

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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.

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