RNA seq data analysis

Question

[suhas]

I have two NCBI TSA files. I want to get differentially expressed genes from this. How can i proceed?

[GouthamAtla]

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[suhas]

Files are of assembled transcriptome of different genotypes of plant. I want to select genes which are differentially expressed in these two genotypes. I want genes which are expressed in plant A but not in plant B

Thank you

[GouthamAtla]

Are they annotated ?

Answer 1

[Michael]

You cannot, at least not easily and using the assembled transcripts only, what you need for differential expression is

1. the transcripts
2. counts for each of the transcripts under different conditions, those counts replicated, to quantify expression

If these were contained in your assembly, fine, you could take those, even though they would not be independent of the assembly. Better, get raw reads data, best independent of the assembly, and map them back to the transcripts.

[suhas]

Thank you Michael.

I will try to get raw reads data of the experiment. I am totally new for this area. How can I process the raw read to get differentially expressed genes at the end?