What file to use for Deseq2 and where to get it from

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1

Hello everyone, I wanted to use Deseq 2 and till now I used the SRA data for mapping and Quality check but I’m not able to do that for Deseq2, can anyone suggest which data to take and how to get that data in Galaxy.

2

Hi @Ashwin_G.k,
it depends on your approach; did you mapped your reads against the genome (e.g. STAR or HISAT2) or did you perform a quasi-mapping approach (e.g. Salmon or Kallisto). I recommend you to have a look at the transcriptomics training material.

Regards

3

Hello Sir, I mapped my reads against the genome using Rna sta, so how do i proceed further and also could you enlighten me if i’m using quasi approach as well?.

4

Hi @Ashwin_G.k,
I recommend you to have a look at these two histories; they describe the whole workflow for mapping the reads by using both RNA STAR and SALMON.

Let me know if you have any doubt.

Regards