annotation and genetic variants

Question

[deeksha3696]

Hey!!

We have differential expressed genes. Now we need to find the markers, genetic variants, and annotations. What should we do to do the further process?

We have RNA seq data of rice from this we extracted differentially expressed genes.

Thank you!

[WouterDeCoster]

we have differential expressed genes. now we need to find the markers, genetic variants, and annotations.

It is unclear which data exactly you have and what you aim to achieve. Please elaborate.

[deeksha3696]

what are molecular markers?

[deeksha3696]

is it SSR ,SNP,MARKER ID,annotation

[Kevin Blighe]

Please paste a small example of the results that you have. Is it just a list of genes?

What do you mean by "markers"? What do you mean by "genetic variants" in the context of differentially expressed genes?

Please put yourself in our situation. You have not helped us to understand what you want to do.

Answer 1

[pltbiotech_tkarthi]

You can try to generate VCF file from your sequences using reference genome sequence and follow this link for more info. A: Allele frequency visualization