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

Question

[ashwing.kofficial]

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.

Answer 1

[ATpoint]

DESeq2 takes as input a matrix of raw counts, with rows being genes or regions (or whatever you quantify against) and columns being the samples. You can download RNA-seq data in fastq format, quantify against a reference and then make a count matrix.

For starters: https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

[ashwing.kofficial]

Hello sir, thanks for the reply,is it possible to do this in Galaxy program as I am well versed with it?

[ATpoint]

Probably, you will need to read the Galaxy documentation or post a question in their support forum, for starters: https://galaxyproject.org/support/